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2J9K
Asym. Unit
Info
Asym.Unit (83 KB)
Biol.Unit 1 (77 KB)
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(1)
Title
:
ATOMIC-RESOLUTION CRYSTAL STRUCTURE OF CHEMICALLY-SYNTHESIZED HIV-1 PROTEASE COMPLEXED WITH INHIBITOR MVT-101
Authors
:
E. Malito, Y. Shen, E. C. B. Johnson, W. J. Tang
Date
:
11 Nov 06 (Deposition) - 28 Aug 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Protease, Hydrolase-Hydrolase Inhibitor Complex, Aspartyl Protease, Human Immunodeficiency Virus 1
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. C. B. Johnson, E. Malito, Y. Shen, B. Pentelute, D. Rich, J. Florian, W. J. Tang, S. B. H. Kent
Insights From Atomic-Resolution X-Ray Structures Of Chemically Synthesized Hiv-1 Protease In Complex With Inhibitors.
J. Mol. Biol. V. 373 573 2007
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Hetero Components
(7, 23)
Info
All Hetero Components
1a: N-{(2S)-2-[(N-ACETYL-L-THREONYL-L-... (2NCa)
2a: ALPHA-AMINOBUTYRIC ACID (ABAa)
2b: ALPHA-AMINOBUTYRIC ACID (ABAb)
2c: ALPHA-AMINOBUTYRIC ACID (ABAc)
2d: ALPHA-AMINOBUTYRIC ACID (ABAd)
3a: ACETATE ION (ACTa)
3b: ACETATE ION (ACTb)
3c: ACETATE ION (ACTc)
3d: ACETATE ION (ACTd)
3e: ACETATE ION (ACTe)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
5a: NORLEUCINE (NLEa)
5b: NORLEUCINE (NLEb)
5c: NORLEUCINE (NLEc)
5d: NORLEUCINE (NLEd)
6a: L-THIALYSINE (SLZa)
6b: L-THIALYSINE (SLZb)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
7d: SULFATE ION (SO4d)
7e: SULFATE ION (SO4e)
View:
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Label:
No.
Name
Count
Type
Full Name
1
2NC
1
Ligand/Ion
N-{(2S)-2-[(N-ACETYL-L-THREONYL-L-ISOLEUCYL)AMINO]HEXYL}-L-NORLEUCYL-L-GLUTAMINYL-N~5~-[AMINO(IMINIO)METHYL]-L-ORNITHINAMIDE
2
ABA
4
Mod. Amino Acid
ALPHA-AMINOBUTYRIC ACID
3
ACT
5
Ligand/Ion
ACETATE ION
4
GOL
2
Ligand/Ion
GLYCEROL
5
NLE
4
Mod. Amino Acid
NORLEUCINE
6
SLZ
2
Mod. Amino Acid
L-THIALYSINE
7
SO4
5
Ligand/Ion
SULFATE ION
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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:
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No.
Name
Evidence
Residues
Description
01
AC1
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 , VAL A:82 , HOH A:2011 , HOH A:2028 , HOH A:2031 , HOH A:2079 , HOH A:2080 , HOH A:2081 , ARG B:8 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , ASP B:30 , GLY B:48 , GLY B:49 , VAL B:82
BINDING SITE FOR RESIDUE 2NC A 0
02
AC2
SOFTWARE
PRO A:1 , ARG A:57 , HIS A:69 , HOH A:2058 , HOH B:2073
BINDING SITE FOR RESIDUE SO4 A 1105
03
AC3
SOFTWARE
GLY A:73 , THR A:74 , ASN A:88 , HOH A:2029 , HOH A:2070
BINDING SITE FOR RESIDUE SO4 A 1106
04
AC4
SOFTWARE
LYS A:7 , ARG A:8 , HOH A:2010
BINDING SITE FOR RESIDUE ACT A 1107
05
AC5
SOFTWARE
LYS A:55 , ARG A:57 , GLY A:68 , HOH A:2038 , HOH A:2052 , HOH A:2056
BINDING SITE FOR RESIDUE ACT A 1108
06
AC6
SOFTWARE
PHE A:99 , HOH A:2060 , HOH A:2078 , NLE B:46 , PHE B:53 , LYS B:55 , HIS B:69 , SO4 B:1107
BINDING SITE FOR RESIDUE GOL A 1109
07
AC7
SOFTWARE
VAL A:11 , THR A:12 , SLZ A:41 , TRP A:42
BINDING SITE FOR RESIDUE GOL A 1110
08
AC8
SOFTWARE
ARG A:14 , HOH A:2016 , ARG B:14 , GLY B:17 , PRO B:63 , HOH B:2055 , HOH B:2075 , HOH B:2076
BINDING SITE FOR RESIDUE SO4 B 1105
09
AC9
SOFTWARE
HIS A:69 , LYS A:70 , HOH A:2060 , PRO B:1 , LYS B:55 , SO4 B:1107
BINDING SITE FOR RESIDUE SO4 B 1106
10
BC1
SOFTWARE
HIS A:69 , GOL A:1109 , HOH A:2059 , PRO B:1 , HIS B:69 , SO4 B:1106 , HOH B:2074
BINDING SITE FOR RESIDUE SO4 B 1107
11
BC2
SOFTWARE
GLY B:73 , THR B:74 , ASN B:88 , GLN B:92 , HOH B:2062 , HOH B:2066
BINDING SITE FOR RESIDUE ACT B 1108
12
BC3
SOFTWARE
ARG B:8
BINDING SITE FOR RESIDUE ACT B 1109
13
BC4
SOFTWARE
LYS A:55 , LYS A:70 , LYS B:70
BINDING SITE FOR RESIDUE ACT B 1110
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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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:
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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_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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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2j9kA00 (A:1-99)
1b: CATH_2j9kB00 (B:1-99)
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Organisms
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)
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)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Cathepsin D, subunit A; domain 1
(745)
Homologous Superfamily
:
Acid Proteases
(745)
[unclassified]
(17)
1a
2j9kA00
A:1-99
1b
2j9kB00
B:1-99
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Pfam Domains
(0, 0)
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Protein
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Protein & NOT Variant
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Protein & NOT PROSITE
Chain A
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Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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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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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (83 KB)
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