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3QO9
Asym. Unit
Info
Asym.Unit (169 KB)
Biol.Unit 1 (164 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX WITH TSAO-T, A NON-NUCLEOSIDE RT INHIBITOR (NNRTI)
Authors
:
K. Das, E. Arnold
Date
:
09 Feb 11 (Deposition) - 04 May 11 (Release) - 19 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Aids, Hiv, Rna-Binding, Rna-Directed Dna Polymerase, Transferase, Viral Nucleoprotein, Nonnucleoside, Nnrti, Hydrolase, Hydrolase- Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Das, J. D. Bauman, A. S. Rim, C. Dharia, A. D. Clark, M. J. Camarasa, J. Balzarini, E. Arnold
Crystal Structure Of Tert-Butyldimethylsilyl-Spiroaminooxathioledioxide-Thymine (Tsao-T) In Complex With Hiv-1 Reverse Transcriptase (Rt) Redefines The Elastic Limits Of The Non-Nucleoside Inhibitor-Binding Pocket.
J. Med. Chem. V. 54 2727 2011
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: 1-[(5R,6R,8R,9R)-4-AMINO-9-{[TERT-... (QO9a)
View:
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Label:
No.
Name
Count
Type
Full Name
1
QO9
1
Ligand/Ion
1-[(5R,6R,8R,9R)-4-AMINO-9-{[TERT-BUTYL(DIMETHYL)SILYL]OXY}-6-({[TERT-BUTYL(DIMETHYL)SILYL]OXY}METHYL)-2,2-DIOXIDO-1,7-DIOXA-2-THIASPIRO[4.4]NON-3-EN-8-YL]-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:95 , LEU A:100 , LYS A:101 , LYS A:102 , LYS A:103 , VAL A:106 , VAL A:179 , TYR A:181 , TYR A:188 , LYS A:220 , PHE A:227 , TRP A:229 , LEU A:234 , HIS A:235 , PRO A:236 , TYR A:318 , HOH A:572 , HOH A:575 , HOH A:579
BINDING SITE FOR RESIDUE QO9 A 556
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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, )
View:
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Label:
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:434-552)
;
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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:434-552
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Exons
(0, 0)
Info
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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
(2, 3)
Info
All SCOP Domains
1a: SCOP_d3qo9a2 (A:430-552)
2a: SCOP_d3qo9a1 (A:0-429)
2b: SCOP_d3qo9b_ (B:)
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Protein Domains
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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
d3qo9a2
A:430-552
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
Reverse transcriptase
(217)
Protein domain
:
HIV-1 reverse transcriptase
(161)
Human immunodeficiency virus type 1 [TaxId: 11676]
(138)
2a
d3qo9a1
A:0-429
2b
d3qo9b_
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
(4, 7)
Info
all PFAM domains
1a: PFAM_RNase_H_3qo9A01 (A:435-552)
2a: PFAM_RVT_1_3qo9B01 (B:63-234)
2b: PFAM_RVT_1_3qo9B02 (B:63-234)
3a: PFAM_RVT_connect_3qo9B03 (B:317-419)
3b: PFAM_RVT_connect_3qo9B04 (B:317-419)
4a: PFAM_RVT_thumb_3qo9B05 (B:238-307)
4b: PFAM_RVT_thumb_3qo9B06 (B:238-307)
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Clans
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(
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(
)
Clan
:
RNase_H
(288)
Family
:
RNase_H
(128)
Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1)
(28)
1a
RNase_H-3qo9A01
A:435-552
Clan
:
RdRP
(210)
Family
:
RVT_1
(95)
Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1)
(27)
2a
RVT_1-3qo9B01
B:63-234
2b
RVT_1-3qo9B02
B:63-234
Clan
:
no clan defined [family: RVT_connect]
(84)
Family
:
RVT_connect
(84)
Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1)
(27)
3a
RVT_connect-3qo9B03
B:317-419
3b
RVT_connect-3qo9B04
B:317-419
Clan
:
no clan defined [family: RVT_thumb]
(84)
Family
:
RVT_thumb
(84)
Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1)
(27)
4a
RVT_thumb-3qo9B05
B:238-307
4b
RVT_thumb-3qo9B06
B:238-307
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Asym.Unit (169 KB)
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