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4DG1
Asym. Unit
Info
Asym.Unit (175 KB)
Biol.Unit 1 (170 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) WITH POLYMORPHISM MUTATION K172A AND K173A
Authors
:
X. Tu, K. A. Kirby, B. Marchand, S. G. Sarafianos
Date
:
24 Jan 12 (Deposition) - 20 Jun 12 (Release) - 12 Sep 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Polymorphism 172K, P51/P66, Hetero Dimer, Aids, Hiv, Resistance Mutations, Right-Hand Configuration, Rnase H Domain, Reverse Transcriptase, Ribonuclease H, Rna-Directed Dna Polymerase, Dna Polymerase, Transferase, Azt Excision, Azt Unblocking, Nevirapine, Efavirenz, Azt, Nucleoside Inhibitors, Nonnucleoside Inhibitors, Nrti, Nnrti
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Hachiya, B. Marchand, K. A. Kirby, E. Michailidis, X. Tu, K. Palczewski, Y. T. Ong, Z. Li, D. T. Griffin, M. M. Schuckmann, J. Tanuma, S. Oka, K. Singh, E. N. Kodama, S. G. Sarafianos
Hiv-1 Reverse Transcriptase (Rt) Polymorphism 172K Suppresses The Effect Of Clinically Relevant Drug Resistanc Mutations To Both Nucleoside And Non-Nucleoside Rt Inhibitors.
J. Biol. Chem. V. 287 29988 2012
[
close entry info
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Hetero Components
(3, 24)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
14
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
6
Ligand/Ion
GLYCEROL
3
MG
4
Ligand/Ion
MAGNESIUM ION
[
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Sites
(24, 24)
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)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:269 , LYS A:350 , THR A:351 , GOL A:607 , HOH A:817
BINDING SITE FOR RESIDUE MG A 601
02
AC2
SOFTWARE
ASP A:443 , GLY A:444 , GLU A:478 , ASP A:498
BINDING SITE FOR RESIDUE MG A 602
03
AC3
SOFTWARE
PRO A:226 , GLU A:233 , HIS A:235 , HOH A:812
BINDING SITE FOR RESIDUE MG A 603
04
AC4
SOFTWARE
VAL A:442 , VAL A:496 , ASP A:498 , ILE A:542 , GLY A:543
BINDING SITE FOR RESIDUE EDO A 604
05
AC5
SOFTWARE
GLU A:44 , LYS A:46 , SER A:117
BINDING SITE FOR RESIDUE EDO A 605
06
AC6
SOFTWARE
LYS A:103 , PRO A:176 , ASP A:177 , ILE A:178 , VAL A:179
BINDING SITE FOR RESIDUE GOL A 606
07
AC7
SOFTWARE
HIS A:96 , TRP A:239 , GLN A:269 , ILE A:270 , VAL A:314 , HIS A:315 , LEU A:349 , LYS A:350 , THR A:351 , MG A:601
BINDING SITE FOR RESIDUE GOL A 607
08
AC8
SOFTWARE
TYR A:532 , ALA A:534 , TRP A:535 , ASN B:255 , GLN B:258 , LYS B:259
BINDING SITE FOR RESIDUE GOL A 608
09
AC9
SOFTWARE
THR A:7 , ASP A:121 , GLU A:122 , ASP A:123
BINDING SITE FOR RESIDUE EDO A 609
10
BC1
SOFTWARE
THR A:386 , THR B:27
BINDING SITE FOR RESIDUE EDO A 610
11
BC2
SOFTWARE
LYS A:395 , GLU A:396 , GLU A:399 , HOH A:747 , HOH A:809
BINDING SITE FOR RESIDUE GOL A 611
12
BC3
SOFTWARE
GLN A:197 , LYS A:201
BINDING SITE FOR RESIDUE EDO A 612
13
BC4
SOFTWARE
LYS A:101 , LYS A:103 , VAL A:106 , TYR A:188 , HIS A:235
BINDING SITE FOR RESIDUE EDO A 613
14
BC5
SOFTWARE
GLU A:370 , GLN A:373 , LYS A:374 , THR A:377 , GLU B:396 , THR B:400
BINDING SITE FOR RESIDUE EDO A 614
15
BC6
SOFTWARE
THR A:377 , PRO B:25 , THR B:400 , EDO B:504
BINDING SITE FOR RESIDUE EDO A 615
16
BC7
SOFTWARE
GLN B:23 , ASN B:57 , THR B:58 , THR B:131
BINDING SITE FOR RESIDUE MG B 501
17
BC8
SOFTWARE
TRP A:406 , GLN B:330 , LYS B:331 , PRO B:392 , VAL B:423
BINDING SITE FOR RESIDUE EDO B 502
18
BC9
SOFTWARE
PRO B:157 , TYR B:183 , MET B:184 , HOH B:604
BINDING SITE FOR RESIDUE EDO B 503
19
CC1
SOFTWARE
EDO A:615 , TRP B:24 , GLU B:399 , TRP B:402 , HOH B:646 , HOH B:704
BINDING SITE FOR RESIDUE EDO B 504
20
CC2
SOFTWARE
ARG B:358 , LYS B:366 , GLU B:370 , TYR B:405 , GLN B:407
BINDING SITE FOR RESIDUE EDO B 505
21
CC3
SOFTWARE
LYS B:30 , LYS B:64 , TRP B:71 , THR B:403 , GLU B:404 , TRP B:406
BINDING SITE FOR RESIDUE GOL B 506
22
CC4
SOFTWARE
HIS A:315 , PHE A:346 , LYS A:347 , ASN A:348 , TYR B:318
BINDING SITE FOR RESIDUE EDO B 507
23
CC5
SOFTWARE
GLU A:6 , THR A:7 , GLU B:53
BINDING SITE FOR RESIDUE GOL B 508
24
CC6
SOFTWARE
GLY B:45 , PRO B:119 , ARG B:125 , ASN B:147 , HOH B:707
BINDING SITE FOR RESIDUE EDO B 509
[
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SAPs(SNPs)/Variants
(5, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_POL_HV1B1_003 (A172R, 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:
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
A
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:434-549)
;
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
A:44-234
B:44-234
2
RNASE_H
PS50879
RNase H domain profile.
POL_HV1B1
1033-1156
1
A:434-549
[
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Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d4dg1a2 (A:430-549)
2a: SCOP_d4dg1a1 (A:1-429)
3a: SCOP_d4dg1b_ (B:)
View:
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Classes
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(
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(
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(
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(
)
Protein Domains
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(
)
Organisms
(
)
(
)
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 [TaxId: 11678]
(14)
1a
d4dg1a2
A:430-549
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 [TaxId: 11678]
(12)
2a
d4dg1a1
A:1-429
Protein domain
:
HIV-1 reverse transcriptase
(161)
Human immunodeficiency virus type 1 [TaxId: 11676]
(138)
3a
d4dg1b_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Asymmetric Unit 1
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