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3NDU
Asym. Unit
Info
Asym.Unit (164 KB)
Biol.Unit 1 (82 KB)
Biol.Unit 2 (80 KB)
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(1)
Title
:
HIV-1 PROTEASE SAQUINAVIR:RITONAVIR 1:5 COMPLEX STRUCTURE
Authors
:
S. Geremia, F. M. Olajuyigbe, N. Demitri
Date
:
08 Jun 10 (Deposition) - 20 Jul 11 (Release) - 07 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.25
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Hiv-1 Protease, Hydrolase, Aids, Aspartyl Protease, Saquinavir, Carbamylation, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. M. Olajuyigbe, N. Demitri, S. Geremia
Investigation Of 2-Fold Disorder Of Inhibitors And Relative Potency By Crystallizations Of Hiv-1 Protease In Ritonavir And Saquinavir Mixtures
Cryst. Growth Des. V. 11 4378 2011
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Hetero Components
(7, 25)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: FORMAMIDE (ARFa)
2b: FORMAMIDE (ARFb)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
3f: CHLORIDE ION (CLf)
4a: DIMETHYL SULFOXIDE (DMSa)
4b: DIMETHYL SULFOXIDE (DMSb)
4c: DIMETHYL SULFOXIDE (DMSc)
4d: DIMETHYL SULFOXIDE (DMSd)
4e: DIMETHYL SULFOXIDE (DMSe)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
6a: SODIUM ION (NAa)
6b: SODIUM ION (NAb)
6c: SODIUM ION (NAc)
7a: (2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)... (ROCa)
7b: (2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)... (ROCb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
4
Ligand/Ion
ACETATE ION
2
ARF
2
Mod. Amino Acid
FORMAMIDE
3
CL
6
Ligand/Ion
CHLORIDE ION
4
DMS
5
Ligand/Ion
DIMETHYL SULFOXIDE
5
GOL
3
Ligand/Ion
GLYCEROL
6
NA
3
Ligand/Ion
SODIUM ION
7
ROC
2
Ligand/Ion
(2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT-BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H-ISOQUINOLIN-2-YL]-3-HYDROXY-1-PHENYL-BUTAN-2-YL]-2-(QUINOLIN-2-YLCARBONYLAMINO)BUTANEDIAMIDE
[
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Sites
(22, 22)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:9 , ASP A:26 , GLY A:28 , ALA A:29 , ASP A:30 , ASP A:31 , ILE A:48 , GLY A:49 , GLY A:50 , ILE A:51 , THR A:81 , PRO A:82 , ILE A:85 , HOH A:119 , HOH A:570 , ARG B:9 , ASP B:26 , GLY B:28 , ALA B:29 , ASP B:30 , ASP B:31 , GLY B:49 , GLY B:50 , ILE B:51 , THR B:81 , PRO B:82 , VAL B:83 , ILE B:85 , HOH B:103 , HOH B:107 , HOH B:153 , TRP C:6
BINDING SITE FOR RESIDUE ROC A 101
02
AC2
SOFTWARE
LYS A:15 , ILE A:16 , GLY A:18 , ILE A:64 , GLY B:18 , DMS B:101
BINDING SITE FOR RESIDUE DMS A 102
03
AC3
SOFTWARE
THR A:13 , GLU A:66 , ALA A:68 , GLY A:69 , NA A:1015
BINDING SITE FOR RESIDUE ACT A 1007
04
AC4
SOFTWARE
LYS B:71
BINDING SITE FOR RESIDUE CL A 1010
05
AC5
SOFTWARE
GLN A:3 , ILE A:4 , THR A:5
BINDING SITE FOR RESIDUE GOL A 1012
06
AC6
SOFTWARE
GLY A:69 , HOH A:112 , ACT A:1007
BINDING SITE FOR RESIDUE NA A 1015
07
AC7
SOFTWARE
TRP A:7 , ARG B:88
BINDING SITE FOR RESIDUE ACT A 1017
08
AC8
SOFTWARE
LYS A:44 , LYS A:46 , GLN A:59
BINDING SITE FOR RESIDUE CL A 1021
09
AC9
SOFTWARE
LYS A:15 , GLY A:18 , DMS A:102 , LYS B:15 , ILE B:16 , GLY B:17 , GLY B:18 , ILE B:64
BINDING SITE FOR RESIDUE DMS B 101
10
BC1
SOFTWARE
LYS B:46 , MET B:47 , HOH B:104 , HOH B:212 , HOH D:107
BINDING SITE FOR RESIDUE GOL B 1001
11
BC2
SOFTWARE
SER B:38
BINDING SITE FOR RESIDUE CL B 1003
12
BC3
SOFTWARE
SER A:38
BINDING SITE FOR RESIDUE CL B 1005
13
BC4
SOFTWARE
ASP B:61
BINDING SITE FOR RESIDUE NA B 1014
14
BC5
SOFTWARE
LEU B:11 , VAL B:12 , THR B:13 , HOH B:576 , TRP C:42
BINDING SITE FOR RESIDUE ACT B 1016
15
BC6
SOFTWARE
HIS A:70 , ILE A:94 , PHE B:100
BINDING SITE FOR RESIDUE NA B 1020
16
BC7
SOFTWARE
LYS C:14 , GLY C:16 , GLY C:17 , ILE C:63 , GLY D:17 , DMS D:101
BINDING SITE FOR RESIDUE DMS C 100
17
BC8
SOFTWARE
MET C:36 , SER C:37 , PRO D:39 , GLY D:40 , HOH D:203
BINDING SITE FOR RESIDUE DMS C 101
18
BC9
SOFTWARE
LYS A:71 , LYS B:15 , LYS C:55
BINDING SITE FOR RESIDUE CL C 1006
19
CC1
SOFTWARE
THR C:4 , TRP C:6 , HOH C:301 , THR D:91 , GLY D:94
BINDING SITE FOR RESIDUE ACT C 1008
20
CC2
SOFTWARE
PRO C:79 , HOH C:578 , GLY D:51 , HOH D:541
BINDING SITE FOR RESIDUE GOL C 1013
21
CC3
SOFTWARE
ARG C:8 , ASP C:25 , GLY C:27 , ALA C:28 , ASP C:29 , ASP C:30 , VAL C:32 , ILE C:47 , GLY C:48 , GLY C:49 , ILE C:50 , THR C:80 , PRO C:81 , ILE C:84 , HOH C:129 , HOH C:573 , ASP D:25 , GLY D:27 , ALA D:28 , ASP D:29 , ASP D:30 , VAL D:32 , ILE D:47 , GLY D:48 , GLY D:49 , ILE D:50 , THR D:80 , PRO D:81 , ILE D:84 , HOH D:115 , HOH D:150
BINDING SITE FOR RESIDUE ROC D 100
22
CC4
SOFTWARE
GLY C:17 , DMS C:100 , LYS D:14 , ILE D:15 , GLY D:16 , GLY D:17 , ILE D:63 , GLU D:65
BINDING SITE FOR RESIDUE DMS D 101
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ASP_PROT_RETROV (A:21-90,B:21-90,C:20-89,D:20-89)
2: ASP_PROTEASE (A:23-33,B:23-33,C:22-32,D:22-32)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ASP_PROT_RETROV
PS50175
Aspartyl protease, retroviral-type family profile.
POL_HV1BR
520-589
4
A:21-90
B:21-90
C:20-89
D:20-89
2
ASP_PROTEASE
PS00141
Eukaryotic and viral aspartyl proteases active site.
POL_HV1BR
522-533
4
A:23-33
B:23-33
C:22-32
D:22-32
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3ndua_ (A:)
1b: SCOP_d3ndub_ (B:)
1c: SCOP_d3nduc_ (C:)
1d: SCOP_d3ndud_ (D:)
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)
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)
Protein Domains
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)
(
)
Organisms
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)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Acid proteases
(1120)
Superfamily
:
Acid proteases
(1120)
Family
:
Retroviral protease (retropepsin)
(591)
Protein domain
:
Human immunodeficiency virus type 1 protease
(514)
Human immunodeficiency virus type 1 [TaxId: 11676]
(424)
1a
d3ndua_
A:
1b
d3ndub_
B:
1c
d3nduc_
C:
1d
d3ndud_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
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Sorry, no Info available
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Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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