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2YKN
Asym. Unit
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Asym.Unit (175 KB)
Biol.Unit 1 (166 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX WITH A DIFLUOROMETHYLBENZOXAZOLE (DFMB) PYRIMIDINE THIOETHER DERIVATIVE, A NON-NUCLEOSIDE RT INHIBITOR (NNRTI)
Authors
:
J. Boyer, E. Arnoult, M. Medebielle, J. Guillemont, T. Unge, J. Unge, D.
Date
:
28 May 11 (Deposition) - 17 Aug 11 (Release) - 14 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.12
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hydrolase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
J. Boyer, E. Arnoult, M. Medebielle, J. Guillemont, J. Unge, D. Jochmans
Difluoromethylbenzoxazole Pyrimidine Thioether Derivatives: A Novel Class Of Potent Non-Nucleoside Hiv-1 Reverse Transcriptase Inhibitors.
J. Med. Chem. V. 54 7974 2011
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: 2-[DIFLUORO-[(4-METHYL-PYRIMIDINYL... (YKNa)
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Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
YKN
1
Ligand/Ion
2-[DIFLUORO-[(4-METHYL-PYRIMIDINYL)-THIO]METHYL]-BENZOXAZOLE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:100 , LYS A:101 , LYS A:103 , VAL A:106 , VAL A:179 , TYR A:181 , TYR A:188 , GLY A:190 , LEU A:234 , HIS A:235 , TYR A:318 , HOH A:2162
BINDING SITE FOR RESIDUE YKN A1559
2
AC2
SOFTWARE
ASP A:443 , GLY A:444 , GLN A:478 , ASP A:498
BINDING SITE FOR RESIDUE CA A1560
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SAPs(SNPs)/Variants
(5, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_POL_HV1B1_003 (K172R, chain A/B, )
2: VAR_POL_HV1B1_004 (K451R, chain A, )
3: VAR_POL_HV1B1_005 (V458L, chain A, )
4: VAR_POL_HV1B1_006 (K512Q, chain A, )
5: VAR_POL_HV1B1_007 (E529Q, chain A, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_POL_HV1B1_003
*
K
771
R
POL_HV1B1
---
---
A/B
K
172
R
2
UniProt
VAR_POL_HV1B1_004
*
K
1050
R
POL_HV1B1
---
---
A
K
451
R
3
UniProt
VAR_POL_HV1B1_005
*
V
1057
L
POL_HV1B1
---
---
A
V
458
L
4
UniProt
VAR_POL_HV1B1_006
*
K
1111
Q
POL_HV1B1
---
---
A
K
512
Q
5
UniProt
VAR_POL_HV1B1_007
*
E
1128
Q
POL_HV1B1
---
---
A
E
529
Q
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 3)
Info
All PROSITE Patterns/Profiles
1: RT_POL (A:44-234,B:44-234)
2: RNASE_H (A:434-557)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RT_POL
PS50878
Reverse transcriptase (RT) catalytic domain profile.
POL_HV1B1
643-833
2
A:44-234
B:44-234
2
RNASE_H
PS50879
RNase H domain profile.
POL_HV1B1
1033-1156
1
A:434-557
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Exons
(0, 0)
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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
(2, 3)
Info
All SCOP Domains
1a: SCOP_d2ykna2 (A:430-558)
2a: SCOP_d2ykna1 (A:1-429)
2b: SCOP_d2yknb_ (B:)
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Protein Domains
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Organisms
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
automated matches
(127)
Protein domain
:
automated matches
(127)
Human immunodeficiency virus type 1 bh10 [TaxId: 11678]
(12)
1a
d2ykna2
A:430-558
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
Reverse transcriptase
(217)
Protein domain
:
automated matches
(34)
Human immunodeficiency virus type 1 bh10 [TaxId: 11678]
(5)
2a
d2ykna1
A:1-429
2b
d2yknb_
B:
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(0, 0)
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Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (175 KB)
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