List of data items in ./5hvp.cif
data_5HVP.
loop_
_atom_site_group_PDB
_atom_site_type_symbol
_atom_site_label_atom_id
_atom_site_label_res_id
_atom_site_label_asym_id
_atom_site_label_seq_id
_atom_site_label_alt_id
_atom_site_Cartn_x
_atom_site_Cartn_y
_atom_site_Cartn_z
_atom_site_occupancy
_atom_site_B_iso_or_equiv
_atom_site_footnote_id
_atom_site_entity_id
_atom_site_entity_seq_num
ATOM
N
N
VAL
A
11
?
25.369
30.691
11.795
1.00
17.93
?
1
11
ATOM
C
CA
VAL
A
11
?
25.970
31.965
12.332
1.00
17.75
?
1
11
ATOM
C
C
VAL
A
11
?
25.569
32.010
13.808
1.00
17.83
?
1
11
ATOM
O
O
VAL
A
11
?
24.735
31.190
14.167
1.00
17.53
?
1
11
ATOM
C
CB
VAL
A
11
?
25.379
33.146
11.540
1.00
17.66
?
1
11
ATOM
C
CG1
VAL
A
11
?
25.584
33.034
10.030
1.00
18.86
?
1
11
ATOM
C
CG2
VAL
A
11
?
23.933
33.309
11.872
1.00
17.12
?
1
11
ATOM
N
N
THR
A
12
?
26.095
32.930
14.590
1.00
18.97
4
1
12
ATOM
C
CA
THR
A
12
?
25.734
32.995
16.032
1.00
19.80
4
1
12
ATOM
C
C
THR
A
12
?
24.695
34.106
16.113
1.00
20.92
4
1
12
ATOM
O
O
THR
A
12
?
24.869
35.118
15.421
1.00
21.84
4
1
12
ATOM
C
CB
THR
A
12
?
26.911
33.346
17.018
1.00
20.51
4
1
12
ATOM
O
OG1
THR
A
12
3
27.946
33.921
16.183
0.50
20.29
4
1
12
ATOM
O
OG1
THR
A
12
4
27.769
32.142
17.103
0.50
20.59
4
1
12
ATOM
C
CG2
THR
A
12
3
27.418
32.181
17.878
0.50
20.47
4
1
12
ATOM
C
CG2
THR
A
12
4
26.489
33.778
18.426
0.50
20.00
4
1
12
ATOM
N
N
ILE
A
13
?
23.664
33.855
16.884
1.00
22.08
?
1
13
ATOM
C
CA
ILE
A
13
?
22.623
34.850
17.093
1.00
23.44
?
1
13
ATOM
C
C
ILE
A
13
?
22.657
35.113
18.610
1.00
25.77
?
1
13
ATOM
O
O
ILE
A
13
?
23.123
34.250
19.406
1.00
26.28
?
1
13
ATOM
C
CB
ILE
A
13
?
21.236
34.463
16.492
1.00
22.67
?
1
13
ATOM
C
CG1
ILE
A
13
?
20.478
33.469
17.371
1.00
22.14
?
1
13
ATOM
C
CG2
ILE
A
13
?
21.357
33.986
15.016
1.00
21.75
?
1
13
ATOM
C
C1
APS
C
300
1
4.171
29.012
7.116
0.58
17.27
1
2
?
ATOM
C
C2
APS
C
300
1
4.949
27.758
6.793
0.58
16.95
1
2
?
ATOM
O
O3
APS
C
300
1
4.800
26.678
7.393
0.58
16.85
1
2
?
ATOM
N
N4
APS
C
300
1
5.930
27.841
5.869
0.58
16.43
1
2
?
_atom_sites_Cartn_transform_axes 'c along z, astar along x, b along y'
_atom_sites_Cartn_tran_matrix_11 58.39
_atom_sites_Cartn_tran_matrix_12 0.00
_atom_sites_Cartn_tran_matrix_13 0.00
_atom_sites_Cartn_tran_matrix_21 0.00
_atom_sites_Cartn_tran_matrix_22 86.70
_atom_sites_Cartn_tran_matrix_23 0.00
_atom_sites_Cartn_tran_matrix_31 0.00
_atom_sites_Cartn_tran_matrix_32 0.00
_atom_sites_Cartn_tran_matrix_33 46.27
_atom_sites_fract_tran_matrix_11 0.017126
_atom_sites_fract_tran_matrix_12 0.000000
_atom_sites_fract_tran_matrix_13 0.000000
_atom_sites_fract_tran_matrix_21 0.000000
_atom_sites_fract_tran_matrix_22 0.011534
_atom_sites_fract_tran_matrix_23 0.000000
_atom_sites_fract_tran_matrix_31 0.000000
_atom_sites_fract_tran_matrix_32 0.000000
_atom_sites_fract_tran_matrix_33 0.021612
loop_
_atom_sites_alt_id
_atom_sites_alt_details
'?'
;
Atom sites with the alternate id set to null are not modelled in alter-
nate conformations
;
'1'
;
Atom sites with the alternate id set to 1 have been modelled in
alternate conformations with respect to atom sites marked with alternate
conformation id 2. The conformations of amino acid side chains
and solvent atoms with alternate id set to 1 correlate with the
conformation of the inhibitor marked with alternate id 1. They
have been given an occupancy of 0.58 to match the occupancy assigned
to the inhibitor.
;
'2'
;
Atom sites with the alternate id set to 2 have been modelled in
alternate conformations with respect to atom sites marked with alternate
conformation id 1. The conformations of amino acid side chains
and solvent atoms with alternate id set to 2 correlate with the
conformation of the inhibitor marked with alternate id 2. They
have been given an occupancy of 0.42 to match the occupancy assigned
to the inhibitor.
;
'3'
;
Atom sites with the alternate id set to 3 have been modelled in
alternate conformations with respect to atoms marked with alternate
conformation id 4. The conformations of amino acid side chains
and solvent atoms with alternate id set to 3 do not correlate with
the conformation of the inhibitor. These atom sites have arbitrarily
been given an occupancy of 0.50.
;
'4'
;
Atom sites with the alternate id set to 4 have been modelled in
alternate conformations with respect to atoms marked with alternate
conformation id 3. The conformations of amino acid side chains
and solvent atoms with alternate id set to 4 do not correlate with
the conformation of the inhibitor. These atom sites have arbitrarily
been given an occupancy of 0.50.
;
loop_
_atom_sites_alt_ens_id
_atom_sites_alt_ens_details
'Ensemble 1-A'
;
The inhibitor binds to the enzyme in two, roughly twofold symmetric,
alternate conformations.
This conformational ensemble includes the more populated conformation of
the inhibitor (id=1) and the amino acid side chains and solvent structure
that correlate with this inhibitor conformation.
Also included are one set (id=3) of side chains with alternate conform-
ations when the conformations are not correlated with the inhibitor
conformation.
;
'Ensemble 1-B'
;
The inhibitor binds to the enzyme in two, roughly twofold symmetric
alternate conformations.
This conformational ensemble includes the more populated conformation of
the inhibitor (id=1) and the amino acid side chains and solvent structure
that correlate with this inhibitor conformation.
Also included are one set (id=4) of side chains with alternate conform-
ations when the conformations are not correlated with the inhibitor
conformation.
;
'Ensemble 2-A'
;
The inhibitor binds to the enzyme in two, roughly twofold symmetric
alternate conformations.
This conformational ensemble includes the less populated conformation of
the inhibitor (id=2) and the amino acid side chains and solvent structure
that correlate with this inhibitor conformation.
Also included are one set (id=3) of side chains with alternate conform-
ations when the conformations are not correlated with the inhibitor
conformation.
;
'Ensemble 2-B'
;
The inhibitor binds to the enzyme in two, roughly twofold symmetric
alternate conformations.
This conformational ensemble includes the less populated conformation of
the inhibitor (id=2) and the amino acid side chains and solvent structure
that correlate with this inhibitor conformation.
Also included are one set (id=4) of side chains with alternate conform-
ations when the conformations are not correlated with the inhibitor
conformation.
;
loop_
_atom_sites_alt_gen_ens_id
_atom_sites_alt_gen_alt_id
'Ensemble 1-A'
'?'
'Ensemble 1-A'
'1'
'Ensemble 1-A'
'3'
'Ensemble 1-B'
'?'
'Ensemble 1-B'
'1'
'Ensemble 1-B'
'4'
'Ensemble 2-A'
'?'
'Ensemble 2-A'
'2'
'Ensemble 2-A'
'3'
'Ensemble 2-B'
'?'
'Ensemble 2-B'
'2'
'Ensemble 2-B'
'4'
loop_
_atom_sites_footnote_id
_atom_sites_footnote_text
1
;
The inhibitor binds to the enzyme in two alternate orientations. The
two orientations have been assigned alternate location indicators *1*
and *2*.
;
2
;
Side chains of these residues adopt alternate orientations that corre-
late with the alternate orientations of the inhibitor.
Side chains with alternate location indicator *1* and occupancy 0.58
correlate with inhibitor orientation *1*.
Side chains with alternate location indicator *2* and occupancy 0.42
correlate with inhibitor orientation *2*.
;
3
;
The positions of these water molecules correlate with the alternate
orientations of the inhibitor.
Water molecules with alternate location indicator *1* and occupancy 0.58
correlate with inhibitor orientation *1*.
Water molecules with alternate location indicator *2* and occupancy 0.42
correlate with inhibitor orientation *2*.
;
4
;
Side chains of these residues adopt alternate orientations that do not
correlate with the alternate orientation of the inhibitor.
;
5
;
The positions of these water molecules correlate with alternate orien-
tations of amino acid side chains that do not correlate with alternate
orientations of the inhibitor.
;
loop_
_atom_type_symbol
_atom_type_oxidation_number
_atom_type_scat_Cromer_Mann_a1
_atom_type_scat_Cromer_Mann_a2
_atom_type_scat_Cromer_Mann_a3
_atom_type_scat_Cromer_Mann_a4
_atom_type_scat_Cromer_Mann_b1
_atom_type_scat_Cromer_Mann_b2
_atom_type_scat_Cromer_Mann_b3
_atom_type_scat_Cromer_Mann_b4
_atom_type_scat_Cromer_Mann_c
C
0
2.31000
20.8439
1.02000
10.2075
1.58860
0.568700
0.865000
51.6512
0.21560
N
0
12.2126
0.005700
3.13220
9.89330
2.01250
28.9975
1.16630
0.582600
-11.529
O
0
3.04850
13.2771
2.28680
5.70110
1.54630
0.323900
0.867000
32.9089
0.250800
S
0
6.90530
1.46790
5.20340
22.2151
1.43790
0.253600
1.58630
56.1720
0.866900
CL
-1
18.2915
0.006600
7.20840
1.17170
6.53370
19.5424
2.33860
60.4486
-16.378
_audit_creation_date '92-12-08'
_audit_creation_method
;
Created by hand from PDB entry 5HVP, from the JBC paper describing this
structure and from laboratory records
;
_audit_update_record
;
92-12-09 adjusted to reflect comments from Brian McKeever
92-12-10 adjusted to reflect comments from Helen Berman
92-12-12 adjusted to reflect comments from Keith Watenpaugh
;
loop_
_audit_author_name
_audit_author_address
'Fitzgerald, Paula M.D.'
;
Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
'McKeever, Brian M.'
;
Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
'Van Middlesworth, J.F.'
;
Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
'Springer, James P.'
;
Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
_audit_contact_author_name 'Fitzgerald, Paula M.D.'
_audit_contact_author_address
;
Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
_audit_contact_author_phone '908 594 5510'
_audit_contact_author_fax '908 594 6645'
_audit_contact_author_email 'paula_fitzgerald@merck.com'
_cell_length_a 58.39(5)
_cell_length_b 86.70(12)
_cell_length_c 46.27(6)
_cell_angle_alpha 90.00
_cell_angle_beta 90.00
_cell_angle_gamma 90.00
_cell_volume 234237
_cell_special_details
;
The cell parameters were refined every twenty frames during data integra-
tion. The cell lengths given are the mean of 55 such refinements; the
esds given are the root mean square deviations of these 55 observations
from that mean.
;
_cell_measurement_temperature 293(3)
_cell_measurement_theta_min 11
_cell_measurement_theta_max 31
_cell_measurement_wavelength 1.54
loop_
_citation_id
_citation_coordinate_linkage
_citation_title
_citation_country
_citation_page_first
_citation_page_last
_citation_year
_citation_journal_abbrev
_citation_journal_volume
_citation_journal_issue
_citation_journal_coden_ASTM
_citation_journal_coden_ISSN
_citation_journal_coden_PDB
_citation_book_title
_citation_book_publisher
_citation_book_coden_ISBN
_citation_special_details
primary
yes
;
Crystallographic analysis of a complex between human immunodeficiency
virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution.
;
US
14209
14219
1990
'J. Biol. Chem.'
265
?
HBCHA3
0021-9258
071
?
?
?
;
The publication that directly relates to this coordinate set.
;
2
no
;
Three-dimensional structure of aspartyl-protease from human
immunodeficiency virus HIV-1.
;
UK
615
619
1989
'Nature'
337
?
NATUAS
0028-0836
006
?
?
?
;
Determination of the structure of the unliganded enzyme.
;
3
no
;
Crystallization of the aspartylprotease from human immunodeficiency virus,
HIV-1.
;
US
1919
1921
1989
'J. Biol. Chem.'
264
?
HBCHA3
0021-9258
071
?
?
?
;
Crystallization of the unliganded enzyme.
;
4
no
;
Human immunodeficiency virus protease. Bacterial expression and
characterization of the purified aspartic protease.
;
US
2307
2312
1989
'J. Biol. Chem.'
264
?
HBCHA3
0021-9258
071
?
?
?
;
Expression and purification of the enzyme.
;
loop_
_citation_author_citation_id
_citation_author_name
primary
'Fitzgerald, P.M.D.'
primary
'McKeever, B.M.'
primary
'Van Middlesworth, J.F.'
primary
'Springer, J.P.'
primary
'Heimbach, J.C.'
primary
'Leu, C.-T.'
primary
'Herber, W.K.'
primary
'Dixon, R.A.F.'
primary
'Darke, P.L.'
2
'Navia, M.A.'
2
'Fitzgerald, P.M.D.'
2
'McKeever, B.M.'
2
'Leu, C.-T.'
2
'Heimbach, J.C.'
2
'Herber, W.K.'
2
'Sigal, I.S.'
2
'Darke, P.L.'
2
'Springer, J.P.'
3
'McKeever, B.M.'
3
'Navia, M.A.'
3
'Fitzgerald, P.M.D.'
3
'Springer, J.P.'
3
'Leu, C.-T.'
3
'Heimbach, J.C.'
3
'Herber, W.K.'
3
'Sigal, I.S.'
3
'Darke, P.L.'
4
'Darke, P.L.'
4
'Leu, C.-T.'
4
'Davis, L.J.'
4
'Heimbach, J.C.'
4
'Diehl, R.E.'
4
'Hill, W.S.'
4
'Dixon, R.A.F.'
4
'Sigal, I.S.'
_computing_data_collection 'Collect (Siemens)'
_computing_data_reduction 'Xengen (Howard)'
_computing_phasing_MR 'Merlot (Fitzgerald)'
_computing_molecular_graphics 'Protein (Steigemann), Frodo (Jones)'
_computing_structure_refinement 'Protin/Prolsq (Konnert, Hendrickson)'
_database_code_PDB 5HVP
loop_
_database_remark_num_PDB
_database_remark_text_PDB
1
REMARK
2
2
REMARK
2
RESOLUTION.
2.0
ANGSTROMS.
3
REMARK
3
4
REMARK
3
REFINEMENT.
BY
THE
RESTRAINED
LEAST-SQUARES
PROCEDURE
OF
J.
5
REMARK
3
KONNERT
AND
W.
HENDRICKSON
(PROGRAM
*PROLSQ*).
THE
R
6
REMARK
3
VALUE
IS
0.176
FOR
12901
REFLECTIONS
IN
THE
RESOLUTION
7
REMARK
3
RANGE
8.0
TO
2.0
ANGSTROMS
WITH
I
.GT.
SIGMA(I).
loop_
_database_rev_num_PDB
_database_rev_author_name_PDB
_database_rev_date_PDB
_database_rev_date_original_PDB
_database_rev_status_PDB
_database_rev_mod_type_PDB
1
'Fitzgerald, Paula M.D'
91-10-15
90-04-30
'full release'
0
_diffrn_ambient_temperature 293(3)
_diffrn_crystal_environment
;
Mother liquor from the reservoir of the vapor diffusion experiment,
mounted in room air
;
_diffrn_crystal_physical_device
;
0.7 mm glass capillary, sealed with dental wax
;
_diffrn_crystal_treatment
;
Equilibrated in rotating anode radiation enclosure for 18 hours prior
to beginning of data collection.
;
_diffrn_measurement_method 'omega scan'
_diffrn_measurement_details
;
440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle
22.5 degrees
;
_diffrn_measure_device_type '3-circle camera'
_diffrn_measure_device_part 'Supper model x'
_diffrn_measure_device_details 'none'
_diffrn_radiation_collimation '0.3 mm double pinhole'
_diffrn_radiation_monochromator graphite
_diffrn_radiation_type 'Cu K\a'
_diffrn_radiation_wavelength 1.54
_diffrn_rad_detector_type 'multiwire'
_diffrn_rad_detector_part 'Siemens'
_diffrn_rad_source_type 'rotating anode'
_diffrn_rad_source_part 'Rigaku RU-200'
_diffrn_rad_source_power '50 kw, 180 mA'
_diffrn_rad_source_target '8mm x 0.4 mm broad-focus'
loop_
_entity_id
_entity_type
_entity_name_common
_entity_name_systematic
_entity_source
_entity_special_details
1
polymer
'HIV-1 protease'
ECx.x.x.x
;
Clone obtained from HIV strain NY-5.
Expressed in E. coli.
;
;
The enzymatically competent form of HIV protease is a
dimer. This entity corresponds to one monomer of an
active dimer.
;
2
non-polymer
'acetyl-pepstatin'
'acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta'
'Natural product isolated from actinomycetes'
;
Statine: ((4S,3S)-4-amino-3-hydroxy-6-methylheptanoic
acid. Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka
Prefecture University, and provided to us by Dr. Ben
Dunn, University of Florida, and Dr. J. Kay, University
of Wales.
;
3
water
'water'
?
?
?
loop_
_entity_keywords_entity_id
_entity_keywords_text
1
'polypeptide'
2
'natural product'
2
'inhibitor'
2
'reduced peptide'
loop_
_entity_nonp_id
_entity_nonp_entity_id
_entity_nonp_formula
_entity_nonp_formula_weight
_entity_nonp_number_of_nh_atoms
_entity_nonp_model_source
_entity_nonp_model_details
APS
2
'C31 H55 N5 O9'
641.8
45
'Built by hand using ChemNote in Quanta (MSI)'
'Geometry idealized using AMF (Merck)'
loop_
_entity_nonp_atom_entity_id
_entity_nonp_atom_atom_id
_entity_nonp_atom_type_symbol
_entity_nonp_atom_model_Cartn_x
_entity_nonp_atom_model_Cartn_y
_entity_nonp_atom_model_Cartn_z
2
1
C
-0.15600
-0.90770
-2.11270
2
2
C
-0.20530
-1.10010
-0.59490
2
3
O
-0.51270
-2.16520
-0.06340
2
4
N
0.09550
-0.00790
0.11530
2
5
C
0.14840
-0.01830
1.58870
2
6
C
1.41550
-0.79710
2.04770
2
7
C
2.71100
-0.17870
1.47350
2
8
C
1.50570
-0.94000
3.58320
2
9
C
0.20050
1.42100
2.12200
2
10
O
0.58080
2.37350
1.43910
2
11
N
-0.15500
1.55910
3.40030
loop_
_entity_nonp_bond_entity_id
_entity_nonp_bond_atom_id_1
_entity_nonp_bond_atom_id_2
_entity_nonp_bond_type
2
1
2
sing
2
2
3
doub
2
2
4
sing
2
4
5
sing
2
5
6
sing
2
5
9
sing
2
6
7
sing
2
6
8
sing
2
9
10
doub
2
9
11
sing
loop_
_entity_poly_entity_id
_entity_poly_type
_entity_poly_formula_weight
_entity_poly_non_s_chirality
_entity_poly_non_s_linkage
_entity_poly_non_s_monomer
_entity_poly_type_details
1
polypeptide(L)
10916
no
no
no
?
loop_
_entity_poly_seq_entity_id
_entity_poly_seq_num
_entity_poly_seq_mon_id
1
1
PRO
1
2
GLN
1
3
ILE
1
4
THR
1
5
LEU
1
6
TRP
1
7
GLN
1
8
ARG
1
9
PRO
1
10
LEU
1
11
VAL
1
12
THR
1
13
ILE
1
14
LYS
1
15
ILE
1
16
GLY
1
17
GLY
1
18
GLN
1
19
LEU
1
20
LYS
1
21
GLU
1
22
ALA
1
23
LEU
1
24
LEU
1
25
ASP
_exptl_crystal_grow_method 'hanging drop'
_exptl_crystal_grow_apparatus 'Linbro plates'
_exptl_crystal_grow_atmosphere 'room air'
_exptl_crystal_grow_pH 4.7
_exptl_crystal_grow_temp 18(3)
_exptl_crystal_grow_time 'approximately 2 days'
loop_
_exptl_crystal_grow_com_id
_exptl_crystal_grow_com_sol_id
_exptl_crystal_grow_com_name
_exptl_crystal_grow_com_volume
_exptl_crystal_grow_com_conc
_exptl_crystal_grow_com_details
1
1
'HIV-1 protease'
'0.002 ml'
'6 mg/ml'
;
The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/
MES buffer, pH 7.5, 3 mM NaAzide
;
2
2
'NaCl'
'0.200 ml'
'4 M'
'in 3 mM NaAzide'
3
2
'Acetic Acid'
'0.047 ml'
'100 mM'
'in 3 mM NaAzide'
4
2
'Na Acetate'
'0.053 ml'
'100 mM'
;
in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7
according to a ratio calculated from the pKa. The actual pH of solution 2
was not measured.
;
5
2
'water'
'0.700 ml'
'neat'
'in 3 mM NaAzide'
_refine_ls_number_reflns 12901
_refine_ls_number_restraints 6609
_refine_ls_number_parameters 7032
_refine_ls_R_Factor_obs 0.176
_refine_ls_weighting_scheme calc
_refine_ls_weighting_details
;
Sigdel model of Konnert-Hendrickson:
Sigdel: Afsig + Bfsig*(sin(theta)/lambda-1/6)
Afsig = 22.0, Bfsig = -150.0 at the beginning of refinement.
Afsig = 15.5, Bfsig = -50.0 at the end of refinement.
;
loop_
_refine_ls_restr_type
_refine_ls_restr_target
_refine_ls_restr_model
_refine_ls_restr_number
_refine_ls_restr_criterion
_refine_ls_restr_rejects
'bond_d'
0.020
0.018
1654
'> 2\s'
22
'angle_d'
0.030
0.038
2246
'> 2\s'
139
'planar_d'
0.040
0.043
498
'> 2\s'
21
'planar'
0.020
0.015
270
'> 2\s'
1
'chiral'
0.150
0.177
278
'> 2\s'
2
'singtor_nbd'
0.500
0.216
582
'> 2\s'
0
'multtor_nbd'
0.500
0.207
419
'> 2\s'
0
'xyhbond_nbd'
0.500
0.245
149
'> 2\s'
0
'planar_tor'
3.0
2.6
203
'> 2\s'
9
'staggered_tor'
15.0
17.4
298
'> 2\s'
31
'orthonormal_tor'
20.0
18.1
12
'> 2\s'
1
loop_
_refine_ls_shell_d_res_low
_refine_ls_shell_d_res_high
_refine_ls_shell_reflns
_refine_ls_shell_R_factor_obs
8.00
4.51
1226
0.196
4.51
3.48
1679
0.146
3.48
2.94
2014
0.160
2.94
2.59
2147
0.182
2.59
2.34
2127
0.193
2.34
2.15
2061
0.203
2.15
2.00
1647
0.188
loop_
_refine_occupancy_class
_refine_occupancy_treatment
_refine_occupancy_value
_refine_occupancy_details
'protein'
fix
1.00
?
'solvent'
fix
1.00
?
'inhibitor orientation 1'
fix
0.65
?
'inhibitor orientation 2'
fix
0.35
;
The inhibitor binds to the enzyme in two alternate conformations. The
occupancy of each conformation was adjusted so as to result in approxi-
mately equal mean thermal factors for the atoms in each conformation.
;
loop_
_refine_B_iso_class
_refine_B_iso_treatment
'protein'
isotropic
'solvent'
isotropic
'inhibitor'
isotropic
_reflns_data_reduction_method
;
Xengen program scalei. Anomalous paris were merged. Scaling proceeded
in several passes, beginning with 1-parameter fit and ending with
3-parameter fit.
;
_reflns_data_reduction_details
;
Merging and scaling based on only those reflections with I > \s(I).
;
_reflns_d_resolution_high 2.00
_reflns_d_resolution_low 8.00
_reflns_limit_h_max 22
_reflns_limit_h_min 0
_reflns_limit_k_max 46
_reflns_limit_k_min 0
_reflns_limit_l_max 57
_reflns_limit_l_min 0
_reflns_number_observed 7228
_reflns_observed_criterion '> 1 \s(I)'
_reflns_special_details none
loop_
_reflns_shell_d_res_high
_reflns_shell_d_res_low
_reflns_shell_meanI/sigI_obs
_reflns_shell_count_measured_obs
_reflns_shell_count_unique_obs
_reflns_shell_possible__obs
_reflns_shell_Rmerge_F_obs
31.38
3.82
69.8
9024
2540
96.8
1.98
3.82
3.03
26.1
7413
2364
95.1
3.85
3.03
2.65
10.5
5640
2123
86.2
6.37
2.65
2.41
6.4
4322
1882
76.8
8.01
2.41
2.23
4.3
3247
1714
70.4
9.86
2.23
2.10
3.1
1140
812
33.3
13.99
_struct_title
;
HIV-1 protease complex with acetyl-pepstatin
;
loop_
_struct_keywords
'enzyme-inhibitor complex'
'aspartyl protease'
'structure-based drug design'
'static disorder'
loop_
_struct_asym_id
_struct_asym_entity_id
_struct_asym_special_details
A
1
'one monomer of the dimeric enzyme'
B
1
'one monomer of the dimeric enzyme'
C
2
'one partially occupied position for the inhibitor'
D
2
'one partially occupied position for the inhibitor'
loop_
_struct_biol_id
_struct_biol_special_details
1
;
significant deviations from twofold symmetry exist in this dimeric
enzyme
;
2
;
The drug binds to this enzyme in two roughly twofold symmetric modes.
Hence this biological unit (2) is roughly twofold symmetric to biological
unit (3). Disorder in the protein chain indicated with alternate
indicator 1 should be used with this biological unit.
;
3
;
The drug binds to this enzyme in two roughly twofold symmetric modes.
Hence this biological unit (3) is roughly twofold symmetric to biological
unit (2). Disorder in the protein chain indicated with alternate
indicator 2 should be used with this biological unit.
;
loop_
_struct_biol_gen_biol_id
_struct_biol_gen_asym_id
_struct_biol_gen_symmetry
1
A
1_555
1
B
1_555
2
A
1_555
2
B
1_555
2
C
1_555
3
A
1_555
3
B
1_555
3
D
1_555
loop_
_struct_biol_keywords_biol_id
_struct_biol_keywords_text
1
'aspartyl-protease'
1
'aspartic-protease'
1
'acid-protease'
1
'aspartyl-proteinase'
1
'aspartic-proteinase'
1
'acid-proteinase'
1
'enzyme'
1
'protease'
1
'proteinase'
1
'dimer'
2
'drug-enzyme complex'
2
'inhibitor-enzyme complex'
2
'drug-protease complex'
2
'inhibitor-protease complex'
3
'drug-enzyme complex'
3
'inhibitor-enzyme complex'
3
'drug-protease complex'
3
'inhibitor-protease complex'
loop_
_struct_conf_id
_struct_conf_conf_type_id
_struct_conf_beg_label_res_id
_struct_conf_beg_label_asym_id
_struct_conf_beg_label_seq_id
_struct_conf_end_label_res_id
_struct_conf_end_label_asym_id
_struct_conf_end_label_seq_id
_struct_conf_special_details
HELX1
HELX-RHAL
ARG
A
87
GLN
A
92
?
HELX2
HELX-RHAL
ARG
B
287
GLN
B
292
?
STRN1
STRN
PRO
A
1
LEU
A
5
?
STRN2
STRN
CYS
B
295
PHE
B
299
?
STRN3
STRN
CYS
A
95
PHE
A
299
?
STRN4
STRN
PRO
B
201
LEU
B
205
?
TURN1
TURN-TY1P
ILE
A
15
GLN
A
18
?
TURN2
TURN-TY2
GLY
A
49
GLY
A
52
?
TURN3
TURN-TY1P
ILE
A
55
HIS
A
69
?
TURN4
TURN-TY1
THR
A
91
GLY
A
94
?
loop_
_struct_conf_type_id
_struct_conf_type_criteria
_struct_conf_type_reference
HELX-RHAL
'author judgement'
?
STRN
'author judgement'
?
TURN-TY1
'author judgement'
?
TURN-TY1P
'author judgement'
?
TURN-TY2
'author judgement'
?
TURN-TY2P
'author judgement'
?
loop_
_struct_conn_id
_struct_conn_conn_type_id
_struct_conn_par1_label_res_id
_struct_conn_par1_label_asym_id
_struct_conn_par1_label_seq_id
_struct_conn_par1_label_atom_id
_struct_conn_role_par1
_struct_conn_symmetry_par1
_struct_conn_par2_label_res_id
_struct_conn_par2_label_asym_id
_struct_conn_par2_label_seq_id
_struct_conn_par2_label_atom_id
_struct_conn_role_par2
_struct_conn_symmetry_par2
_struct_conn_special_details
C1
saltbr
ARG
A
87
NZ1
positive
1_555
GLU
A
92
OE1
negative
1_555
?
C2
hydrog
ARG
B
287
N
donor
1_555
GLY
B
292
O
acceptor
1_555
?
loop_
_struct_conn_type_id
_struct_conn_type_criteria
_struct_conn_type_reference
saltbr
'negative to positive distance > 2.5 \%A, < 3.2 \&A'
?
hydrog
'N to O distance > 2.5 \%A, < 3.5 \&A, N O C angle < 120 degrees'
?
loop_
_struct_site_id
_struct_site_special_details
'P2 site C'
;
residues with a contact < 3.7 \%A to an atom in the P2 moiety of the
inhibitor in the conformation with _struct_asym_id = C
;
'P2 site D'
;
residues with a contact < 3.7 \%A to an atom in the P1 moiety of the
inhibitor in the conformation with _struct_asym_id = D)
;
loop_
_struct_site_gen_id
_struct_site_gen_site_id
_struct_site_gen_label_res_id
_struct_site_gen_label_asym_id
_struct_site_gen_label_seq_id
_struct_site_gen_symmetry
_struct_site_gen_special_details
1
1
VAL
A
32
1_555
?
2
1
ILE
A
47
1_555
?
3
1
VAL
A
82
1_555
?
4
1
ILE
A
84
1_555
?
5
2
VAL
B
232
1_555
?
6
2
ILE
B
247
1_555
?
7
2
VAL
B
282
1_555
?
8
2
ILE
B
284
1_555
?
loop_
_struct_site_keywords_site_id
_struct_site_keywords_text
'P2 site C'
'binding site'
'P2 site C'
'binding pocket'
'P2 site C'
'P2 site'
'P2 site C'
'P2 pocket'
'P2 site D'
'binding site'
'P2 site D'
'binding pocket'
'P2 site D'
'P2 site'
'P2 site D'
'P2 pocket'
_symmetry_cell_setting orthorhombic
_symmetry_Int_Tables_number 18
_symmetry_space_group_name_H-M 'P 21 21 2'
loop_
_symmetry_equiv_pos_as_xyz
+x,+y,+z
-x,-y,z
1/2+x,1/2-y,-z
1/2-x,1/2+y,-z