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3DLG
Asym. Unit
Info
Asym.Unit (168 KB)
Biol.Unit 1 (163 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH GW564511.
Authors
:
J. Ren, P. P. Chamberlain, D. K. Stammers
Date
:
27 Jun 08 (Deposition) - 12 Aug 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hiv-1 Reverse Transcriptase, Aids, Nnrti, Gw564511, Drug Resistance, Transferase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Ren, P. P. Chamberlain, A. Stamp, S. A. Short, K. L. Weaver, K. R. Romines, R. Hazen, A. Freeman, R. G. Ferris, C. W. Andrews, L. Boone, J. H. Chan, D. K. Stammers
Structural Basis For The Improved Drug Resistance Profile Of New Generation Benzophenone Non-Nucleoside Hiv-1 Reverse Transcriptase Inhibitors.
J. Med. Chem. V. 51 5000 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 4)
Info
All Hetero Components
1a: 3-SULFINOALANINE (CSDa)
2a: N-{4-[AMINO(DIHYDROXY)-LAMBDA~4~-S... (GWEa)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSD
1
Mod. Amino Acid
3-SULFINOALANINE
2
GWE
1
Ligand/Ion
N-{4-[AMINO(DIHYDROXY)-LAMBDA~4~-SULFANYL]-2-METHYLPHENYL}-2-(4-CHLORO-2-{[3-FLUORO-5-(TRIFLUOROMETHYL)PHENYL]CARBONYL}PHENOXY)ACETAMIDE
3
PO4
2
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG B:356 , ARG B:358 , GLY B:359
BINDING SITE FOR RESIDUE PO4 B 1300
2
AC2
SOFTWARE
GLY A:436 , ALA A:437 , ASN A:460 , ARG A:461
BINDING SITE FOR RESIDUE PO4 A 1301
3
AC3
SOFTWARE
PRO A:95 , LEU A:100 , LYS A:101 , LYS A:102 , LYS A:103 , LYS A:104 , SER A:105 , TYR A:181 , TYR A:188 , GLY A:190 , PRO A:225 , PHE A:227 , TRP A:229 , LEU A:234 , HIS A:235 , PRO A:236 , TYR A:318
BINDING SITE FOR RESIDUE GWE A 999
[
close Site info
]
SAPs(SNPs)/Variants
(82, 148)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_POL_HV1H2_069 (M41L, chain A/B, )
02: VAR_POL_HV1H2_070 (E44A, chain A/B, )
03: VAR_POL_HV1H2_071 (E44D, chain A/B, )
04: VAR_POL_HV1H2_072 (P52R, chain A/B, )
05: VAR_POL_HV1H2_073 (N54D, chain A/B, )
06: VAR_POL_HV1H2_074 (A62V, chain A/B, )
07: VAR_POL_HV1H2_084 (T69A, chain B, )
08: VAR_POL_HV1H2_085 (T69D, chain B, )
09: VAR_POL_HV1H2_086 (T69G, chain B, )
10: VAR_POL_HV1H2_087 (T69N, chain B, )
11: VAR_POL_HV1H2_088 (K70E, chain A/B, )
12: VAR_POL_HV1H2_089 (K70R, chain A/B, )
13: VAR_POL_HV1H2_090 (K70S, chain A/B, )
14: VAR_POL_HV1H2_091 (L74I, chain A/B, )
15: VAR_POL_HV1H2_092 (L74V, chain A/B, )
16: VAR_POL_HV1H2_093 (V75I, chain A/B, )
17: VAR_POL_HV1H2_094 (V75L, chain A/B, )
18: VAR_POL_HV1H2_095 (V75M, chain A/B, )
19: VAR_POL_HV1H2_096 (V75T, chain A/B, )
20: VAR_POL_HV1H2_097 (F77L, chain A/B, )
21: VAR_POL_HV1H2_098 (W88G, chain A, )
22: VAR_POL_HV1H2_099 (W88S, chain A, )
23: VAR_POL_HV1H2_100 (E89G, chain A, )
24: VAR_POL_HV1H2_101 (E89K, chain A, )
25: VAR_POL_HV1H2_102 (L92I, chain A, )
26: VAR_POL_HV1H2_103 (L100I, chain A/B, )
27: VAR_POL_HV1H2_104 (K101E, chain A/B, )
28: VAR_POL_HV1H2_105 (K101P, chain A/B, )
29: VAR_POL_HV1H2_106 (K101Q, chain A/B, )
30: VAR_POL_HV1H2_107 (K103E, chain A/B, )
31: VAR_POL_HV1H2_108 (K103N, chain A/B, )
32: VAR_POL_HV1H2_109 (K103R, chain A/B, )
33: VAR_POL_HV1H2_110 (V106A, chain A/B, )
34: VAR_POL_HV1H2_111 (V106I, chain A/B, )
35: VAR_POL_HV1H2_112 (V106M, chain A/B, )
36: VAR_POL_HV1H2_113 (V108I, chain A/B, )
37: VAR_POL_HV1H2_114 (Y115F, chain A/B, )
38: VAR_POL_HV1H2_115 (F116Y, chain A/B, )
39: VAR_POL_HV1H2_116 (V118I, chain A/B, )
40: VAR_POL_HV1H2_117 (P119S, chain A/B, )
41: VAR_POL_HV1H2_118 (I135L, chain A/B, )
42: VAR_POL_HV1H2_119 (I135M, chain A/B, )
43: VAR_POL_HV1H2_120 (I135T, chain A/B, )
44: VAR_POL_HV1H2_121 (E138K, chain A/B, )
45: VAR_POL_HV1H2_122 (Q145M, chain A/B, )
46: VAR_POL_HV1H2_123 (Q151M, chain A/B, )
47: VAR_POL_HV1H2_124 (S156A, chain A/B, )
48: VAR_POL_HV1H2_125 (P157S, chain A/B, )
49: VAR_POL_HV1H2_126 (Q161L, chain A/B, )
50: VAR_POL_HV1H2_127 (V179D, chain A/B, )
51: VAR_POL_HV1H2_128 (Y181C, chain A/B, )
52: VAR_POL_HV1H2_129 (M184I, chain A/B, )
53: VAR_POL_HV1H2_130 (M184T, chain A/B, )
54: VAR_POL_HV1H2_131 (M184V, chain A/B, )
55: VAR_POL_HV1H2_132 (Y188C, chain A/B, )
56: VAR_POL_HV1H2_133 (Y188H, chain A/B, )
57: VAR_POL_HV1H2_134 (Y188L, chain A/B, )
58: VAR_POL_HV1H2_135 (V189I, chain A/B, )
59: VAR_POL_HV1H2_136 (G190A, chain A/B, )
60: VAR_POL_HV1H2_137 (G190C, chain A/B, )
61: VAR_POL_HV1H2_138 (G190E, chain A/B, )
62: VAR_POL_HV1H2_139 (G190Q, chain A/B, )
63: VAR_POL_HV1H2_140 (G190S, chain A/B, )
64: VAR_POL_HV1H2_141 (G190T, chain A/B, )
65: VAR_POL_HV1H2_142 (G190V, chain A/B, )
66: VAR_POL_HV1H2_143 (H208Y, chain A/B, )
67: VAR_POL_HV1H2_144 (L210W, chain A/B, )
68: VAR_POL_HV1H2_145 (R211K, chain A/B, )
69: VAR_POL_HV1H2_146 (L214F, chain A, )
70: VAR_POL_HV1H2_147 (T215F, chain A, )
71: VAR_POL_HV1H2_148 (T215Y, chain A, )
72: VAR_POL_HV1H2_149 (K219E, chain A, )
73: VAR_POL_HV1H2_150 (K219Q, chain A, )
74: VAR_POL_HV1H2_151 (K219R, chain A, )
75: VAR_POL_HV1H2_152 (P225H, chain A, )
76: VAR_POL_HV1H2_153 (P236L, chain A/B, )
77: VAR_POL_HV1H2_154 (K238T, chain A/B, )
78: VAR_POL_HV1H2_155 (L283I, chain A/B, )
79: VAR_POL_HV1H2_156 (Y318F, chain A/B, )
80: VAR_POL_HV1H2_157 (G333D, chain A/B, )
81: VAR_POL_HV1H2_158 (G333E, chain A/B, )
82: VAR_POL_HV1H2_159 (T386I, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_POL_HV1H2_069
*
M
628
L
POL_HV1H2
---
---
A/B
M
41
L
02
UniProt
VAR_POL_HV1H2_070
*
E
631
A
POL_HV1H2
---
---
A/B
E
44
A
03
UniProt
VAR_POL_HV1H2_071
*
E
631
D
POL_HV1H2
---
---
A/B
E
44
D
04
UniProt
VAR_POL_HV1H2_072
*
P
639
R
POL_HV1H2
---
---
A/B
P
52
R
05
UniProt
VAR_POL_HV1H2_073
*
N
641
D
POL_HV1H2
---
---
A/B
N
54
D
06
UniProt
VAR_POL_HV1H2_074
*
A
649
V
POL_HV1H2
---
---
A/B
A
62
V
07
UniProt
VAR_POL_HV1H2_084
*
T
656
A
POL_HV1H2
---
---
B
T
69
A
08
UniProt
VAR_POL_HV1H2_085
*
T
656
D
POL_HV1H2
---
---
B
T
69
D
09
UniProt
VAR_POL_HV1H2_086
*
T
656
G
POL_HV1H2
---
---
B
T
69
G
10
UniProt
VAR_POL_HV1H2_087
*
T
656
N
POL_HV1H2
---
---
B
T
69
N
11
UniProt
VAR_POL_HV1H2_088
*
K
657
E
POL_HV1H2
---
---
A/B
K
70
E
12
UniProt
VAR_POL_HV1H2_089
*
K
657
R
POL_HV1H2
---
---
A/B
K
70
R
13
UniProt
VAR_POL_HV1H2_090
*
K
657
S
POL_HV1H2
---
---
A/B
K
70
S
14
UniProt
VAR_POL_HV1H2_091
*
L
661
I
POL_HV1H2
---
---
A/B
L
74
I
15
UniProt
VAR_POL_HV1H2_092
*
L
661
V
POL_HV1H2
---
---
A/B
L
74
V
16
UniProt
VAR_POL_HV1H2_093
*
V
662
I
POL_HV1H2
---
---
A/B
V
75
I
17
UniProt
VAR_POL_HV1H2_094
*
V
662
L
POL_HV1H2
---
---
A/B
V
75
L
18
UniProt
VAR_POL_HV1H2_095
*
V
662
M
POL_HV1H2
---
---
A/B
V
75
M
19
UniProt
VAR_POL_HV1H2_096
*
V
662
T
POL_HV1H2
---
---
A/B
V
75
T
20
UniProt
VAR_POL_HV1H2_097
*
F
664
L
POL_HV1H2
---
---
A/B
F
77
L
21
UniProt
VAR_POL_HV1H2_098
*
W
675
G
POL_HV1H2
---
---
A
W
88
G
22
UniProt
VAR_POL_HV1H2_099
*
W
675
S
POL_HV1H2
---
---
A
W
88
S
23
UniProt
VAR_POL_HV1H2_100
*
E
676
G
POL_HV1H2
---
---
A
E
89
G
24
UniProt
VAR_POL_HV1H2_101
*
E
676
K
POL_HV1H2
---
---
A
E
89
K
25
UniProt
VAR_POL_HV1H2_102
*
L
679
I
POL_HV1H2
---
---
A
L
92
I
26
UniProt
VAR_POL_HV1H2_103
*
L
687
I
POL_HV1H2
---
---
A/B
L
100
I
27
UniProt
VAR_POL_HV1H2_104
*
K
688
E
POL_HV1H2
---
---
A/B
K
101
E
28
UniProt
VAR_POL_HV1H2_105
*
K
688
P
POL_HV1H2
---
---
A/B
K
101
P
29
UniProt
VAR_POL_HV1H2_106
*
K
688
Q
POL_HV1H2
---
---
A/B
K
101
Q
30
UniProt
VAR_POL_HV1H2_107
*
K
690
E
POL_HV1H2
---
---
A/B
K
103
E
31
UniProt
VAR_POL_HV1H2_108
*
K
690
N
POL_HV1H2
---
---
A/B
K
103
N
32
UniProt
VAR_POL_HV1H2_109
*
K
690
R
POL_HV1H2
---
---
A/B
K
103
R
33
UniProt
VAR_POL_HV1H2_110
*
V
693
A
POL_HV1H2
---
---
A/B
V
106
A
34
UniProt
VAR_POL_HV1H2_111
*
V
693
I
POL_HV1H2
---
---
A/B
V
106
I
35
UniProt
VAR_POL_HV1H2_112
*
V
693
M
POL_HV1H2
---
---
A/B
V
106
M
36
UniProt
VAR_POL_HV1H2_113
*
V
695
I
POL_HV1H2
---
---
A/B
V
108
I
37
UniProt
VAR_POL_HV1H2_114
*
Y
702
F
POL_HV1H2
---
---
A/B
Y
115
F
38
UniProt
VAR_POL_HV1H2_115
*
F
703
Y
POL_HV1H2
---
---
A/B
F
116
Y
39
UniProt
VAR_POL_HV1H2_116
*
V
705
I
POL_HV1H2
---
---
A/B
V
118
I
40
UniProt
VAR_POL_HV1H2_117
*
P
706
S
POL_HV1H2
---
---
A/B
P
119
S
41
UniProt
VAR_POL_HV1H2_118
*
I
722
L
POL_HV1H2
---
---
A/B
I
135
L
42
UniProt
VAR_POL_HV1H2_119
*
I
722
M
POL_HV1H2
---
---
A/B
I
135
M
43
UniProt
VAR_POL_HV1H2_120
*
I
722
T
POL_HV1H2
---
---
A/B
I
135
T
44
UniProt
VAR_POL_HV1H2_121
*
E
725
K
POL_HV1H2
---
---
A/B
E
138
K
45
UniProt
VAR_POL_HV1H2_122
*
Q
732
M
POL_HV1H2
---
---
A/B
Q
145
M
46
UniProt
VAR_POL_HV1H2_123
*
Q
738
M
POL_HV1H2
---
---
A/B
Q
151
M
47
UniProt
VAR_POL_HV1H2_124
*
S
743
A
POL_HV1H2
---
---
A/B
S
156
A
48
UniProt
VAR_POL_HV1H2_125
*
P
744
S
POL_HV1H2
---
---
A/B
P
157
S
49
UniProt
VAR_POL_HV1H2_126
*
Q
748
L
POL_HV1H2
---
---
A/B
Q
161
L
50
UniProt
VAR_POL_HV1H2_127
*
V
766
D
POL_HV1H2
---
---
A/B
V
179
D
51
UniProt
VAR_POL_HV1H2_128
*
Y
768
C
POL_HV1H2
---
---
A/B
Y
181
C
52
UniProt
VAR_POL_HV1H2_129
*
M
771
I
POL_HV1H2
---
---
A/B
M
184
I
53
UniProt
VAR_POL_HV1H2_130
*
M
771
T
POL_HV1H2
---
---
A/B
M
184
T
54
UniProt
VAR_POL_HV1H2_131
*
M
771
V
POL_HV1H2
---
---
A/B
M
184
V
55
UniProt
VAR_POL_HV1H2_132
*
Y
775
C
POL_HV1H2
---
---
A/B
Y
188
C
56
UniProt
VAR_POL_HV1H2_133
*
Y
775
H
POL_HV1H2
---
---
A/B
Y
188
H
57
UniProt
VAR_POL_HV1H2_134
*
Y
775
L
POL_HV1H2
---
---
A/B
Y
188
L
58
UniProt
VAR_POL_HV1H2_135
*
V
776
I
POL_HV1H2
---
---
A/B
V
189
I
59
UniProt
VAR_POL_HV1H2_136
*
G
777
A
POL_HV1H2
---
---
A/B
G
190
A
60
UniProt
VAR_POL_HV1H2_137
*
G
777
C
POL_HV1H2
---
---
A/B
G
190
C
61
UniProt
VAR_POL_HV1H2_138
*
G
777
E
POL_HV1H2
---
---
A/B
G
190
E
62
UniProt
VAR_POL_HV1H2_139
*
G
777
Q
POL_HV1H2
---
---
A/B
G
190
Q
63
UniProt
VAR_POL_HV1H2_140
*
G
777
S
POL_HV1H2
---
---
A/B
G
190
S
64
UniProt
VAR_POL_HV1H2_141
*
G
777
T
POL_HV1H2
---
---
A/B
G
190
T
65
UniProt
VAR_POL_HV1H2_142
*
G
777
V
POL_HV1H2
---
---
A/B
G
190
V
66
UniProt
VAR_POL_HV1H2_143
*
H
795
Y
POL_HV1H2
---
---
A/B
H
208
Y
67
UniProt
VAR_POL_HV1H2_144
*
L
797
W
POL_HV1H2
---
---
A/B
L
210
W
68
UniProt
VAR_POL_HV1H2_145
*
R
798
K
POL_HV1H2
---
---
A/B
R
211
K
69
UniProt
VAR_POL_HV1H2_146
*
L
801
F
POL_HV1H2
---
---
A
L
214
F
70
UniProt
VAR_POL_HV1H2_147
*
T
802
F
POL_HV1H2
---
---
A
T
215
F
71
UniProt
VAR_POL_HV1H2_148
*
T
802
Y
POL_HV1H2
---
---
A
T
215
Y
72
UniProt
VAR_POL_HV1H2_149
*
K
806
E
POL_HV1H2
---
---
A
K
219
E
73
UniProt
VAR_POL_HV1H2_150
*
K
806
Q
POL_HV1H2
---
---
A
K
219
Q
74
UniProt
VAR_POL_HV1H2_151
*
K
806
R
POL_HV1H2
---
---
A
K
219
R
75
UniProt
VAR_POL_HV1H2_152
*
P
812
H
POL_HV1H2
---
---
A
P
225
H
76
UniProt
VAR_POL_HV1H2_153
*
P
823
L
POL_HV1H2
---
---
A/B
P
236
L
77
UniProt
VAR_POL_HV1H2_154
*
K
825
T
POL_HV1H2
---
---
A/B
K
238
T
78
UniProt
VAR_POL_HV1H2_155
*
L
870
I
POL_HV1H2
---
---
A/B
L
283
I
79
UniProt
VAR_POL_HV1H2_156
*
Y
905
F
POL_HV1H2
---
---
A/B
Y
318
F
80
UniProt
VAR_POL_HV1H2_157
*
G
920
D
POL_HV1H2
---
---
A/B
G
333
D
81
UniProt
VAR_POL_HV1H2_158
*
G
920
E
POL_HV1H2
---
---
A/B
G
333
E
82
UniProt
VAR_POL_HV1H2_159
*
T
973
I
POL_HV1H2
---
---
A/B
T
386
I
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 4)
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All PROSITE Patterns/Profiles
1: RT_POL (A:44-234,B:44-234)
2: RNASE_H (A:434-539,B:434-437)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RT_POL
PS50878
Reverse transcriptase (RT) catalytic domain profile.
POL_HV1H2
631-821
2
A:44-234
B:44-234
2
RNASE_H
PS50879
RNase H domain profile.
POL_HV1H2
1021-1144
2
A:434-539
B:434-437
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Exons
(0, 0)
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SCOP Domains
(2, 3)
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All SCOP Domains
1a: SCOP_d3dlga2 (A:430-539)
2a: SCOP_d3dlga1 (A:1-429)
2b: SCOP_d3dlgb_ (B:)
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
Ribonuclease H
(190)
Protein domain
:
HIV RNase H (Domain of reverse transcriptase)
(110)
Hiv-1 m:b_hxb2r [TaxId: 11706]
(8)
1a
d3dlga2
A:430-539
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)
Hiv-1 m:b_hxb2r [TaxId: 11706]
(22)
2a
d3dlga1
A:1-429
2b
d3dlgb_
B:
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CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_3dlgB02 (B:99-115,B:157-233)
1b: CATH_3dlgA03 (A:226-319)
1c: CATH_3dlgB03 (B:234-319)
1d: CATH_3dlgA04 (A:320-426)
1e: CATH_3dlgB04 (B:320-426)
1f: CATH_3dlgA02 (A:91-115,A:157-225)
2a: CATH_3dlgA05 (A:427-538)
3a: CATH_3dlgB01 (B:7-95,B:116-156)
3b: CATH_3dlgA01 (A:1-90,A:116-156)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.270, no name defined]
(278)
Hiv-1 m:b_hxb2r. Hiv-1. Organism_taxid: 11706. Strain: hxb2 isolate.
(5)
1a
3dlgB02
B:99-115,B:157-233
1b
3dlgA03
A:226-319
1c
3dlgB03
B:234-319
1d
3dlgA04
A:320-426
1e
3dlgB04
B:320-426
1f
3dlgA02
A:91-115,A:157-225
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
Hiv-1 m:b_hxb2r. Hiv-1. Organism_taxid: 11706. Strain: hxb2 isolate.
(5)
2a
3dlgA05
A:427-538
Architecture
:
Roll
(3276)
Topology
:
HIV Type 1 Reverse Transcriptase; Chain A, domain 1
(164)
Homologous Superfamily
:
HIV Type 1 Reverse Transcriptase, subunit A, domain 1
(164)
Hiv-1 m:b_hxb2r. Hiv-1. Organism_taxid: 11706. Strain: hxb2 isolate.
(5)
3a
3dlgB01
B:7-95,B:116-156
3b
3dlgA01
A:1-90,A:116-156
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Pfam Domains
(0, 0)
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