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3EBZ
Asym. Unit
Info
Asym.Unit (84 KB)
Biol.Unit 1 (79 KB)
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(1)
Title
:
HIGH RESOLUTION HIV-2 PROTEASE STRUCTURE IN COMPLEX WITH CLINICAL DRUG DARUNAVIR
Authors
:
A. Y. Kovalevsky, I. T. Weber
Date
:
28 Aug 08 (Deposition) - 16 Sep 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hiv-2, Aspartic Protease, Inhibitor, Protease-Drug Complex, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Y. Kovalevsky, J. M. Louis, A. Aniana, A. K. Ghosh, I. T. Weber
Structural Evidence For Effectiveness Of Darunavir And Two Related Antiviral Inhibitors Against Hiv-2 Protease
J. Mol. Biol. V. 384 178 2008
[
close entry info
]
Hetero Components
(5, 25)
Info
All Hetero Components
1a: (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]F... (017a)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
2h: CHLORIDE ION (CLh)
3a: IMIDAZOLE (IMDa)
3b: IMIDAZOLE (IMDb)
3c: IMIDAZOLE (IMDc)
3d: IMIDAZOLE (IMDd)
3e: IMIDAZOLE (IMDe)
3f: IMIDAZOLE (IMDf)
4a: SODIUM ION (NAa)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
5e: ZINC ION (ZNe)
5f: ZINC ION (ZNf)
5g: ZINC ION (ZNg)
5h: ZINC ION (ZNh)
5i: ZINC ION (ZNi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
017
1
Ligand/Ion
(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE
2
CL
8
Ligand/Ion
CHLORIDE ION
3
IMD
6
Ligand/Ion
IMIDAZOLE
4
NA
1
Ligand/Ion
SODIUM ION
5
ZN
9
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(25, 25)
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)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:2 , PHE A:3 , LEU A:99 , ZN A:403 , CL A:503 , HOH A:1011 , HOH A:1148
BINDING SITE FOR RESIDUE IMD A 304
02
AC2
SOFTWARE
TYR A:14 , GLY A:17 , GLU A:63 , GLU A:65 , ZN A:406
BINDING SITE FOR RESIDUE IMD A 306
03
AC3
SOFTWARE
LYS A:7 , LEU A:99 , IMD A:304 , CL A:503 , HOH A:1009 , HOH A:1010 , HOH A:1011
BINDING SITE FOR RESIDUE ZN A 403
04
AC4
SOFTWARE
ASP A:79 , HOH A:1029 , HOH A:1030 , GLU B:137
BINDING SITE FOR RESIDUE ZN A 405
05
AC5
SOFTWARE
GLU A:65 , IMD A:306 , HOH A:1007
BINDING SITE FOR RESIDUE ZN A 406
06
AC6
SOFTWARE
SER A:4 , LEU A:99 , IMD A:304 , ZN A:403 , HOH A:1010 , HOH A:1011 , HOH A:1105
BINDING SITE FOR RESIDUE CL A 503
07
AC7
SOFTWARE
ASN A:40 , ASN A:41 , PRO A:44 , HOH A:1067 , HOH A:1090 , HOH A:1109 , ASN B:140
BINDING SITE FOR RESIDUE NA A 601
08
AC8
SOFTWARE
ASP A:25 , GLY A:27 , ALA A:28 , ASP A:30 , ILE A:32 , GLY A:48 , GLY A:49 , ILE A:82 , ILE A:84 , ASP B:125 , GLY B:127 , ALA B:128 , ASP B:129 , ASP B:130 , GLY B:148 , GLY B:149 , ILE B:150 , HOH B:1017
BINDING SITE FOR RESIDUE 017 B 201
09
AC9
SOFTWARE
GLU B:121 , ILE B:146 , PHE B:153 , ASN B:155 , ASP B:179 , IMD B:302 , ZN B:401
BINDING SITE FOR RESIDUE IMD B 301
10
BC1
SOFTWARE
GLU B:121 , PHE B:153 , ASP B:179 , IMD B:301 , ZN B:401 , HOH B:1153
BINDING SITE FOR RESIDUE IMD B 302
11
BC2
SOFTWARE
ASP B:130 , ILE B:146 , MET B:176 , ZN B:402 , ZN B:409 , CL B:501 , CL B:502 , CL B:507
BINDING SITE FOR RESIDUE IMD B 303
12
BC3
SOFTWARE
ARG A:8 , PRO A:81 , TRP B:106 , ZN B:404 , CL B:505 , CL B:506 , HOH B:1061
BINDING SITE FOR RESIDUE IMD B 305
13
BC4
SOFTWARE
GLU B:121 , ASP B:179 , IMD B:301 , IMD B:302
BINDING SITE FOR RESIDUE ZN B 401
14
BC5
SOFTWARE
ASP B:130 , IMD B:303 , ZN B:409 , CL B:502 , HOH B:1002
BINDING SITE FOR RESIDUE ZN B 402
15
BC6
SOFTWARE
IMD B:305 , CL B:505 , CL B:506 , HOH B:1004 , HOH B:1006
BINDING SITE FOR RESIDUE ZN B 404
16
BC7
SOFTWARE
GLU B:165 , CL B:504 , HOH B:1003 , HOH B:1005 , HOH B:1008
BINDING SITE FOR RESIDUE ZN B 407
17
BC8
SOFTWARE
GLU B:158 , CL B:507 , HOH B:1001 , HOH B:1170
BINDING SITE FOR RESIDUE ZN B 408
18
BC9
SOFTWARE
ASP B:130 , IMD B:303 , ZN B:402 , CL B:508 , HOH B:1002
BINDING SITE FOR RESIDUE ZN B 409
19
CC1
SOFTWARE
VAL B:111 , THR B:112 , LYS B:145 , ILE B:146 , IMD B:303 , HOH B:1050
BINDING SITE FOR RESIDUE CL B 501
20
CC2
SOFTWARE
LYS B:107 , GLY B:148 , IMD B:303 , ZN B:402
BINDING SITE FOR RESIDUE CL B 502
21
CC3
SOFTWARE
GLY A:39 , GLY B:117 , ZN B:407
BINDING SITE FOR RESIDUE CL B 504
22
CC4
SOFTWARE
SER B:104 , LEU B:105 , TRP B:106 , LYS B:107 , IMD B:305 , ZN B:404
BINDING SITE FOR RESIDUE CL B 505
23
CC5
SOFTWARE
IMD B:305 , ZN B:404 , HOH B:1006 , HOH B:1112
BINDING SITE FOR RESIDUE CL B 506
24
CC6
SOFTWARE
LYS B:145 , GLU B:158 , IMD B:303 , ZN B:408 , HOH B:1133
BINDING SITE FOR RESIDUE CL B 507
25
CC7
SOFTWARE
ASP B:130 , ZN B:409 , HOH B:1002
BINDING SITE FOR RESIDUE CL B 508
[
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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, 4)
Info
All PROSITE Patterns/Profiles
1: ASP_PROT_RETROV (A:20-89,B:120-189)
2: ASP_PROTEASE (A:22-33,B:122-133)
;
View:
Select:
Label:
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_HV2RO
533-602
2
A:20-89
B:120-189
2
ASP_PROTEASE
PS00141
Eukaryotic and viral aspartyl proteases active site.
POL_HV2RO
535-546
2
A:22-33
B:122-133
[
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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, 2)
Info
All SCOP Domains
1a: SCOP_d3ebza_ (A:)
1b: SCOP_d3ebzb_ (B:)
View:
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Label:
Classes
(
)
(
)
Folds
(
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(
)
Superfamilies
(
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(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Acid proteases
(1120)
Superfamily
:
Acid proteases
(1120)
Family
:
Retroviral protease (retropepsin)
(591)
Protein domain
:
Human immunodeficiency virus type 2 (HIV-2) protease
(18)
Human immunodeficiency virus type 2 (isolate rod) [TaxId: 11720]
(3)
1a
d3ebza_
A:
1b
d3ebzb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3ebzA00 (A:1-99)
1b: CATH_3ebzB00 (B:101-199)
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Cathepsin D, subunit A; domain 1
(745)
Homologous Superfamily
:
Acid Proteases
(745)
Human immunodeficiency virus type 2 (isolate rod). Organism_taxid: 11720.
(3)
1a
3ebzA00
A:1-99
1b
3ebzB00
B:101-199
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Atom Selection
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Protein & NOT Site
Protein & NOT PROSITE
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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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