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2YKN
Biol. Unit 1
Info
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:
[
Gene Ontology, PubMed, Web (Google)
]
)
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
(1, 1)
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 only available for the asymmetric unit)
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)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
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)
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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Asym.Unit (175 KB)
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