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2JE4
Asym. Unit
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Asym.Unit (169 KB)
Biol.Unit 1 (83 KB)
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Title
:
ATOMIC-RESOLUTION CRYSTAL STRUCTURE OF CHEMICALLY-SYNTHESIZED HIV-1 PROTEASE IN COMPLEX WITH JG-365
Authors
:
E. Malito, E. C. B. Johnson, W. J. Tang
Date
:
15 Jan 07 (Deposition) - 28 Aug 07 (Release) - 08 Feb 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.07
Chains
:
Asym. Unit : A,B,C (2 x)
Biol. Unit 1: A,B,C (1x)
Keywords
:
Protease, Hydrolase, High Resolution, Aspartyl Protease, Human Immunodeficiency Virus 1, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. C. B. Johnson, E. Malito, Y. Shen, D. Rich, W. J. Tang, S. B. Kent
Modular Total Chemical Synthesis Of A Human Immunodeficiency Virus Type 1 Protease.
J. Am. Chem. Soc. V. 129 11480 2007
[
close entry info
]
Hetero Components
(7, 20)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: (2Z)-2-AMINOBUT-2-ENOIC ACID (DBUa)
2b: (2Z)-2-AMINOBUT-2-ENOIC ACID (DBUb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
4a: 1-[(2S,3S)-3-AMINO-2-HYDROXY-4-PHE... (JG3a)
5a: NORLEUCINE (NLEa)
5b: NORLEUCINE (NLEb)
5c: NORLEUCINE (NLEc)
5d: NORLEUCINE (NLEd)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
7a: METHYL L-VALINATE (VMEa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
4
Ligand/Ion
ACETATE ION
2
DBU
2
Mod. Amino Acid
(2Z)-2-AMINOBUT-2-ENOIC ACID
3
GOL
3
Ligand/Ion
GLYCEROL
4
JG3
1
Mod. Amino Acid
1-[(2S,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]-L-PROLINE
5
NLE
4
Mod. Amino Acid
NORLEUCINE
6
SO4
5
Ligand/Ion
SULFATE ION
7
VME
1
Mod. Amino Acid
METHYL L-VALINATE
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:42 , PRO A:44 , GLU A:65 , GLY A:68
BINDING SITE FOR RESIDUE ACT A 1100
02
AC2
SOFTWARE
GLU A:21 , VAL A:82 , ASN A:83 , HOH A:2059 , HOH A:2061
BINDING SITE FOR RESIDUE ACT A 1101
03
AC3
SOFTWARE
PHE A:99 , HOH A:2201 , HOH A:2202 , HOH A:2203 , HOH A:2204 , PHE B:53 , LYS B:55 , HIS B:69 , ACT B:1100 , SO4 B:1103
BINDING SITE FOR RESIDUE GOL A 1102
04
AC4
SOFTWARE
THR A:12 , LYS A:41 , TRP A:42 , HOH A:2032 , HOH A:2033
BINDING SITE FOR RESIDUE GOL A 1103
05
AC5
SOFTWARE
GLN A:2 , HOH A:2205 , HOH A:2206 , HOH A:2207 , HOH A:2208 , HOH A:2209 , HOH A:2210 , HOH A:2211 , HOH A:2212 , PRO B:44 , VAL B:56 , ARG B:57
BINDING SITE FOR RESIDUE GOL A 1104
06
AC6
SOFTWARE
PRO A:1 , ASN A:37 , ARG A:57 , HIS A:69 , SO4 A:1109 , HOH A:2213 , HOH A:2214
BINDING SITE FOR RESIDUE SO4 A 1105
07
AC7
SOFTWARE
PRO A:1 , HIS A:69 , SO4 A:1105 , PHE B:99
BINDING SITE FOR RESIDUE SO4 A 1109
08
AC8
SOFTWARE
HOH A:2039 , HOH A:2080 , HOH A:2122 , HOH A:2215 , ARG B:14 , ILE B:15 , GLY B:16 , GLY B:17 , PRO B:63 , SO4 B:1102
BINDING SITE FOR RESIDUE SO4 A 1112
09
AC9
SOFTWARE
LYS A:70 , GOL A:1102 , LYS B:55 , SO4 B:1103 , HOH B:2170 , HOH B:2171
BINDING SITE FOR RESIDUE ACT B 1100
10
BC1
SOFTWARE
LYS A:55 , LYS A:70 , ARG B:14 , LYS B:70
BINDING SITE FOR RESIDUE ACT B 1101
11
BC2
SOFTWARE
ARG A:14 , GLY A:17 , SO4 A:1112 , HOH A:2040 , HOH A:2042 , HOH A:2080 , HOH A:2215 , ILE B:15 , GLY B:16 , GLY B:17 , PRO B:63
BINDING SITE FOR RESIDUE SO4 B 1102
12
BC3
SOFTWARE
HIS A:69 , GOL A:1102 , HOH A:2157 , HOH A:2158 , PRO B:1 , HIS B:69 , ACT B:1100 , HOH B:2168 , HOH B:2169 , HOH B:2172 , HOH B:2173
BINDING SITE FOR RESIDUE SO4 B 1103
13
BC4
SOFTWARE
ARG A:8 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , ILE A:47 , GLY A:48 , GLY A:49 , ILE A:50 , ILE A:84 , HOH A:2107 , HOH A:2112 , HOH A:2116 , HOH A:2117 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , VAL B:32 , GLY B:48 , GLY B:49 , VAL B:82 , ILE B:84 , HOH B:2098 , HOH B:2099
BINDING SITE FOR CHAIN C OF INHIBITOR MOLECULE JG365
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available in "Model" view)
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:20-89)
2: ASP_PROTEASE (A:22-32,B:22-32)
;
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_HV1A2
510-579
2
A:20-89
B:20-89
2
ASP_PROTEASE
PS00141
Eukaryotic and viral aspartyl proteases active site.
POL_HV1A2
512-523
2
A:22-32
B: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, 2)
Info
All SCOP Domains
1a: SCOP_d2je4a_ (A:)
1b: SCOP_d2je4b_ (B:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Acid proteases
(1120)
Superfamily
:
Acid proteases
(1120)
Family
:
Retroviral protease (retropepsin)
(591)
Protein domain
:
automated matches
(39)
Human immunodeficiency virus 1 [TaxId: 11676]
(17)
1a
d2je4a_
A:
1b
d2je4b_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2je4A00 (A:1-99)
1b: CATH_2je4B00 (B:1-99)
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Topologies
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Homologous Superfamilies
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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 1. Organism_taxid: 11676.
(1)
1a
2je4A00
A:1-99
1b
2je4B00
B:1-99
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_RVP_2je4B01 (B:4-98)
1b: PFAM_RVP_2je4B02 (B:4-98)
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(
)
Clan
:
Peptidase_AA
(368)
Family
:
RVP
(212)
Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2) (HIV-1)
(34)
1a
RVP-2je4B01
B:4-98
1b
RVP-2je4B02
B:4-98
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Chain C
Asymmetric Unit 1
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