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3KLE
Biol. Unit 2
Info
Asym.Unit (730 KB)
Biol.Unit 1 (190 KB)
Biol.Unit 2 (188 KB)
Biol.Unit 3 (187 KB)
Biol.Unit 4 (186 KB)
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Title
:
CRYSTAL STRUCTURE OF AZT-RESISTANT HIV-1 REVERSE TRANSCRIPTASE CROSSLINKED TO A DSDNA WITH A BOUND EXCISION PRODUCT, AZTPPPPA
Authors
:
X. Tu, K. Das, S. G. Sarafianos, E. Arnold
Date
:
07 Nov 09 (Deposition) - 22 Sep 10 (Release) - 12 Jan 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Biol. Unit 4: M,N,O,P (1x)
Keywords
:
Azt Resistance Mechanism, Hiv-1, Reverse Transcriptase, Rt, Azt, Resistance Mutations, P51/P66, Nucleoside Inhibitor, Nucleotide Excision, Thymidine Analog Mutations, Aids, Hiv, Dna Polymerase, Nrti, Nrti Resistance, Aztppppa, Aztp4A, Azt Adenosine Dinucleoside Tetraphosphate, Dna-Directed Dna Polymerase, Endonuclease, Hydrolase, Magnesium, Metal-Binding, Multifunctional Enzyme, Myristate, Nuclease, Rna-Directed Dna Polymerase, Transferase, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Tu, K. Das, Q. Han, J. D. Bauman, A. D. Clark, X. Hou, Y. V. Frenkel, B. L. Gaffney, R. A. Jones, P. L. Boyer, S. H. Hughes, S. G. Sarafianos, E. Arnold
Structural Basis Of Hiv-1 Resistance To Azt By Excision.
Nat. Struct. Mol. Biol. V. 17 1202 2010
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Hetero Components
(4, 4)
Info
All Hetero Components
1a: 2',3'-DIDEOXYADENOSINE-5'-MONOPHOS... (2DAa)
1b: 2',3'-DIDEOXYADENOSINE-5'-MONOPHOS... (2DAb)
1c: 2',3'-DIDEOXYADENOSINE-5'-MONOPHOS... (2DAc)
1d: 2',3'-DIDEOXYADENOSINE-5'-MONOPHOS... (2DAd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
4a: N2-(3-MERCAPTOPROPYL)-2'-DEOXYGUAN... (MRGa)
4b: N2-(3-MERCAPTOPROPYL)-2'-DEOXYGUAN... (MRGb)
4c: N2-(3-MERCAPTOPROPYL)-2'-DEOXYGUAN... (MRGc)
4d: N2-(3-MERCAPTOPROPYL)-2'-DEOXYGUAN... (MRGd)
5a: ALPHA-D-FRUCTOFURANOSYL ALPHA-D-GL... (SWEa)
6a: [[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-... (ZP4a)
6b: [[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-... (ZP4b)
6c: [[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-... (ZP4c)
6d: [[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-... (ZP4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2DA
1
Mod. Nucleotide
2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE
2
GOL
1
Ligand/Ion
GLYCEROL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
MRG
1
Mod. Nucleotide
N2-(3-MERCAPTOPROPYL)-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
5
SWE
-1
Ligand/Ion
ALPHA-D-FRUCTOFURANOSYL ALPHA-D-GLUCOPYRANOSIDE
6
ZP4
1
Ligand/Ion
[[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL] [(2S,3S,5R)-3-AZIDO-5-(5-METHYL-2,4-DIOXO-PYRIMIDIN-1-YL)OXOLAN-2-YL]METHYL HYDROGEN PHOSPHATE
[
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Sites
(5, 5)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
5: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
ASP E:110 , VAL E:111 , ASP E:185 , ZP4 E:823
BINDING SITE FOR RESIDUE MG E 600
2
AC6
SOFTWARE
ASP E:443 , GLU E:478 , ASP E:498
BINDING SITE FOR RESIDUE MG E 602
3
AC7
SOFTWARE
LYS E:65 , ARG E:70 , ARG E:72 , ASP E:110 , VAL E:111 , ASP E:113 , ALA E:114 , TYR E:115 , PHE E:116 , GLN E:151 , ASP E:185 , TYR E:215 , PRO E:217 , GLN E:219 , MG E:600 , DA G:705 , 2DA H:822
BINDING SITE FOR RESIDUE ZP4 E 823
4
AC8
SOFTWARE
ARG F:78
BINDING SITE FOR RESIDUE GOL F 438
5
BC3
SOFTWARE
ARG E:211 , ILE J:5 , SER J:117 , VAL J:118 , PRO J:119 , SER J:163 , ILE J:167 , TRP J:212 , LEU J:214 , HOH J:447
BINDING SITE FOR RESIDUE SWE J 438
[
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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 E/F, )
2: VAR_POL_HV1B1_004 (K451R, chain E, )
3: VAR_POL_HV1B1_005 (V458L, chain E, )
4: VAR_POL_HV1B1_006 (K512Q, chain E, )
5: VAR_POL_HV1B1_007 (E529Q, chain E, )
View:
Select:
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
---
---
E/F
K
172
R
2
UniProt
VAR_POL_HV1B1_004
*
K
1050
R
POL_HV1B1
---
---
E
K
451
R
3
UniProt
VAR_POL_HV1B1_005
*
V
1057
L
POL_HV1B1
---
---
E
V
458
L
4
UniProt
VAR_POL_HV1B1_006
*
K
1111
Q
POL_HV1B1
---
---
E
K
512
Q
5
UniProt
VAR_POL_HV1B1_007
*
E
1128
Q
POL_HV1B1
---
---
E
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 (E:44-234,F:44-234)
2: RNASE_H (E:434-557)
;
View:
Select:
Label:
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
-
-
E:44-234
F:44-234
-
-
-
-
2
RNASE_H
PS50879
RNase H domain profile.
POL_HV1B1
1033-1156
1
-
-
E:434-557
-
-
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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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
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(4, 28)
Info
all PFAM domains
1a: PFAM_RNase_H_3kleM01 (M:435-557)
1b: PFAM_RNase_H_3kleM02 (M:435-557)
1c: PFAM_RNase_H_3kleM03 (M:435-557)
1d: PFAM_RNase_H_3kleM04 (M:435-557)
2a: PFAM_RVT_1_3kleN01 (N:63-234)
2b: PFAM_RVT_1_3kleN02 (N:63-234)
2c: PFAM_RVT_1_3kleN03 (N:63-234)
2d: PFAM_RVT_1_3kleN04 (N:63-234)
2e: PFAM_RVT_1_3kleN05 (N:63-234)
2f: PFAM_RVT_1_3kleN06 (N:63-234)
2g: PFAM_RVT_1_3kleN07 (N:63-234)
2h: PFAM_RVT_1_3kleN08 (N:63-234)
3a: PFAM_RVT_connect_3kleN09 (N:317-419)
3b: PFAM_RVT_connect_3kleN10 (N:317-419)
3c: PFAM_RVT_connect_3kleN11 (N:317-419)
3d: PFAM_RVT_connect_3kleN12 (N:317-419)
3e: PFAM_RVT_connect_3kleN13 (N:317-419)
3f: PFAM_RVT_connect_3kleN14 (N:317-419)
3g: PFAM_RVT_connect_3kleN15 (N:317-419)
3h: PFAM_RVT_connect_3kleN16 (N:317-419)
4a: PFAM_RVT_thumb_3kleN17 (N:238-307)
4b: PFAM_RVT_thumb_3kleN18 (N:238-307)
4c: PFAM_RVT_thumb_3kleN19 (N:238-307)
4d: PFAM_RVT_thumb_3kleN20 (N:238-307)
4e: PFAM_RVT_thumb_3kleN21 (N:238-307)
4f: PFAM_RVT_thumb_3kleN22 (N:238-307)
4g: PFAM_RVT_thumb_3kleN23 (N:238-307)
4h: PFAM_RVT_thumb_3kleN24 (N:238-307)
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Clans
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(
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Families
(
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(
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Organisms
(
)
(
)
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-3kleM01
M:435-557
1b
RNase_H-3kleM02
M:435-557
1c
RNase_H-3kleM03
M:435-557
1d
RNase_H-3kleM04
M:435-557
Clan
:
RdRP
(210)
Family
:
RVT_1
(95)
Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1)
(27)
2a
RVT_1-3kleN01
N:63-234
2b
RVT_1-3kleN02
N:63-234
2c
RVT_1-3kleN03
N:63-234
2d
RVT_1-3kleN04
N:63-234
2e
RVT_1-3kleN05
N:63-234
2f
RVT_1-3kleN06
N:63-234
2g
RVT_1-3kleN07
N:63-234
2h
RVT_1-3kleN08
N: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-3kleN09
N:317-419
3b
RVT_connect-3kleN10
N:317-419
3c
RVT_connect-3kleN11
N:317-419
3d
RVT_connect-3kleN12
N:317-419
3e
RVT_connect-3kleN13
N:317-419
3f
RVT_connect-3kleN14
N:317-419
3g
RVT_connect-3kleN15
N:317-419
3h
RVT_connect-3kleN16
N: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-3kleN17
N:238-307
4b
RVT_thumb-3kleN18
N:238-307
4c
RVT_thumb-3kleN19
N:238-307
4d
RVT_thumb-3kleN20
N:238-307
4e
RVT_thumb-3kleN21
N:238-307
4f
RVT_thumb-3kleN22
N:238-307
4g
RVT_thumb-3kleN23
N:238-307
4h
RVT_thumb-3kleN24
N:238-307
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Asym.Unit (730 KB)
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