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3KLE
Asym. Unit
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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(1)
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
[
close entry info
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Hetero Components
(6, 23)
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
4
Mod. Nucleotide
2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE
2
GOL
2
Ligand/Ion
GLYCEROL
3
MG
8
Ligand/Ion
MAGNESIUM ION
4
MRG
4
Mod. Nucleotide
N2-(3-MERCAPTOPROPYL)-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
5
SWE
1
Ligand/Ion
ALPHA-D-FRUCTOFURANOSYL ALPHA-D-GLUCOPYRANOSIDE
6
ZP4
4
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
[
close Hetero Component info
]
Sites
(15, 15)
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)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:110 , VAL A:111 , ASP A:185 , ZP4 A:823
BINDING SITE FOR RESIDUE MG A 600
02
AC2
SOFTWARE
ASP A:443 , GLY A:444 , GLU A:478 , ASP A:498 , HOH A:561
BINDING SITE FOR RESIDUE MG A 602
03
AC3
SOFTWARE
GLU A:44 , LYS A:65 , ARG A:70 , ARG A:72 , ASP A:110 , VAL A:111 , ASP A:113 , ALA A:114 , TYR A:115 , PHE A:116 , GLN A:151 , ASP A:185 , TYR A:215 , PRO A:217 , GLN A:219 , MG A:600 , DA C:705 , 2DA D:822
BINDING SITE FOR RESIDUE ZP4 A 823
04
AC4
SOFTWARE
GLU B:413
BINDING SITE FOR RESIDUE GOL B 438
05
AC5
SOFTWARE
ASP E:110 , VAL E:111 , ASP E:185 , ZP4 E:823
BINDING SITE FOR RESIDUE MG E 600
06
AC6
SOFTWARE
ASP E:443 , GLU E:478 , ASP E:498
BINDING SITE FOR RESIDUE MG E 602
07
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
08
AC8
SOFTWARE
ARG F:78
BINDING SITE FOR RESIDUE GOL F 438
09
AC9
SOFTWARE
ASP I:110 , VAL I:111 , ASP I:185 , ZP4 I:823
BINDING SITE FOR RESIDUE MG I 600
10
BC1
SOFTWARE
ASP I:443 , GLY I:444 , GLU I:478 , ASP I:498 , HOH I:561
BINDING SITE FOR RESIDUE MG I 602
11
BC2
SOFTWARE
GLU I:44 , LYS I:65 , ARG I:70 , ARG I:72 , ASP I:110 , VAL I:111 , ASP I:113 , ALA I:114 , TYR I:115 , PHE I:116 , GLN I:151 , ASP I:185 , TYR I:215 , PRO I:217 , MG I:600 , DA K:705 , 2DA L:822
BINDING SITE FOR RESIDUE ZP4 I 823
12
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
13
BC4
SOFTWARE
ASP M:110 , VAL M:111 , ASP M:185 , ZP4 M:823
BINDING SITE FOR RESIDUE MG M 600
14
BC5
SOFTWARE
ASP M:443 , GLU M:478 , ASP M:498
BINDING SITE FOR RESIDUE MG M 602
15
BC6
SOFTWARE
GLU M:44 , LYS M:46 , LYS M:65 , ARG M:70 , ARG M:72 , ASP M:110 , VAL M:111 , GLY M:112 , ASP M:113 , ALA M:114 , TYR M:115 , PHE M:116 , GLN M:151 , ASP M:185 , PRO M:217 , MG M:600 , DA O:705 , 2DA P:822
BINDING SITE FOR RESIDUE ZP4 M 823
[
close Site info
]
SAPs(SNPs)/Variants
(5, 24)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_POL_HV1B1_003 (K172R, chain A/B/E/F/I/J/M/N, )
2: VAR_POL_HV1B1_004 (K451R, chain A/E/I/M, )
3: VAR_POL_HV1B1_005 (V458L, chain A/E/I/M, )
4: VAR_POL_HV1B1_006 (K512Q, chain A/E/I/M, )
5: VAR_POL_HV1B1_007 (E529Q, chain A/E/I/M, )
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
---
---
A/B/E/F/I/J/M/N
K
172
R
2
UniProt
VAR_POL_HV1B1_004
*
K
1050
R
POL_HV1B1
---
---
A/E/I/M
K
451
R
3
UniProt
VAR_POL_HV1B1_005
*
V
1057
L
POL_HV1B1
---
---
A/E/I/M
V
458
L
4
UniProt
VAR_POL_HV1B1_006
*
K
1111
Q
POL_HV1B1
---
---
A/E/I/M
K
512
Q
5
UniProt
VAR_POL_HV1B1_007
*
E
1128
Q
POL_HV1B1
---
---
A/E/I/M
E
529
Q
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 13)
Info
All PROSITE Patterns/Profiles
1: RT_POL (A:44-234,B:44-234,E:44-234,F:44-23...)
2: RNASE_H (A:434-557,B:430-430,E:434-557,I:43...)
;
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
8
A:44-234
B:44-234
E:44-234
F:44-234
I:44-234
J:44-234
M:44-234
N:44-234
2
RNASE_H
PS50879
RNase H domain profile.
POL_HV1B1
1033-1156
5
A:434-557
B:430-430
E:434-557
I:434-557
M:434-557
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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:
Select:
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)
View:
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Clans
(
)
(
)
Families
(
)
(
)
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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