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1T03
Biol. Unit 1
Info
Asym.Unit (260 KB)
Biol.Unit 1 (251 KB)
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(1)
Title
:
HIV-1 REVERSE TRANSCRIPTASE CROSSLINKED TO TENOFOVIR TERMINATED TEMPLATE-PRIMER (COMPLEX P)
Authors
:
S. Tuske, S. G. Sarafianos, J. Ding, E. Arnold
Date
:
07 Apr 04 (Deposition) - 11 May 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,H,L,P,T
Biol. Unit 1: A,B,H,L,P,T (1x)
Keywords
:
Hiv-1 Rt, Tenofovir, Rt-Dna Complex, Transferase/Antibody/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Tuske, S. G. Sarafianos, A. D. Clark Jr. , J. Ding, L. K. Naeger, K. L. White, M. D. Miller, C. S. Gibbs, P. L. Boyer, P. Clark, G. Wang, B. L. Gaffney, R. A. Jones, D. M. Jerina, S. H. Hughes, E. Arnold
Structure Of Hiv-1 Rt-Dna Complexes Before And After Incorporation Of The Anti-Aids Drug Tenofovir
Nat. Struct. Mol. Biol. V. 11 469 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
2a: N2-(3-MERCAPTOPROPYL)-2'-DEOXYGUAN... (MRGa)
3a: [2-(6-AMINO-9H-PURIN-9-YL)-1-METHY... (TFOa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
MRG
1
Mod. Nucleotide
N2-(3-MERCAPTOPROPYL)-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
3
TFO
1
Mod. Nucleotide
[2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYLPHOSPHONIC ACID
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:443 , GLU A:478 , ASP A:498
BINDING SITE FOR RESIDUE MG A 559
[
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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 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
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
(3, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (L:192-198)
2: RT_POL (A:44-234,B:44-234)
3: RNASE_H (A:434-557)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGKC_MOUSE
84-90
1
L:192-198
2
RT_POL
PS50878
Reverse transcriptase (RT) catalytic domain profile.
POL_HV1B1
643-833
2
A:44-234
B:44-234
3
RNASE_H
PS50879
RNase H domain profile.
POL_HV1B1
1033-1156
1
A: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.
(no "Exon" information available for biological units yet)
SCOP Domains
(6, 7)
Info
All SCOP Domains
1a: SCOP_d1t03h2 (H:124-225)
2a: SCOP_d1t03l2 (L:108-211)
3a: SCOP_d1t03h1 (H:1-123)
4a: SCOP_d1t03l1 (L:1-107)
5a: SCOP_d1t03a1 (A:430-558)
6a: SCOP_d1t03a2 (A:1-429)
6b: SCOP_d1t03b_ (B:)
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Classes
(
)
(
)
Folds
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Mouse (Mus musculus) [TaxId: 10090]
(414)
1a
d1t03h2
H:124-225
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Mouse (Mus musculus) [TaxId: 10090]
(345)
2a
d1t03l2
L:108-211
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Mouse (Mus musculus), cluster 6 [TaxId: 10090]
(12)
3a
d1t03h1
H:1-123
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Mouse (Mus musculus), cluster 4 [TaxId: 10090]
(211)
4a
d1t03l1
L:1-107
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)
Human immunodeficiency virus type 1 [TaxId: 11676]
(101)
5a
d1t03a1
A:430-558
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)
6a
d1t03a2
A:1-429
6b
d1t03b_
B:
[
close SCOP info
]
CATH Domains
(4, 13)
Info
all CATH domains
1a: CATH_1t03A02 (A:91-115,A:157-225)
1b: CATH_1t03B03 (B:238-319)
1c: CATH_1t03A03 (A:226-319)
1d: CATH_1t03A04 (A:320-426)
1e: CATH_1t03B04 (B:320-429)
1f: CATH_1t03B02 (B:94-115,B:157-237)
2a: CATH_1t03A05 (A:427-556)
3a: CATH_1t03B01 (B:1-93,B:116-156)
3b: CATH_1t03A01 (A:1-90,A:116-156)
4a: CATH_1t03L02 (L:108-211)
4b: CATH_1t03H01 (H:1-123)
4c: CATH_1t03L01 (L:1-107)
4d: CATH_1t03H02 (H:124-220)
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)
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)
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)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
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)
[unclassified]
(58)
1a
1t03A02
A:91-115,A:157-225
1b
1t03B03
B:238-319
1c
1t03A03
A:226-319
1d
1t03A04
A:320-426
1e
1t03B04
B:320-429
1f
1t03B02
B:94-115,B:157-237
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
[unclassified]
(102)
2a
1t03A05
A:427-556
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)
[unclassified]
(24)
3a
1t03B01
B:1-93,B:116-156
3b
1t03A01
A:1-90,A:116-156
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
[unclassified]
(54)
4a
1t03L02
L:108-211
4b
1t03H01
H:1-123
4c
1t03L01
L:1-107
4d
1t03H02
H:124-220
[
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]
Pfam Domains
(4, 7)
Info
all PFAM domains
1a: PFAM_RNase_H_1t03A01 (A:435-557)
2a: PFAM_RVT_1_1t03B01 (B:63-234)
2b: PFAM_RVT_1_1t03B02 (B:63-234)
3a: PFAM_RVT_connect_1t03B03 (B:317-419)
3b: PFAM_RVT_connect_1t03B04 (B:317-419)
4a: PFAM_RVT_thumb_1t03B05 (B:238-307)
4b: PFAM_RVT_thumb_1t03B06 (B:238-307)
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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-1t03A01
A: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_1-1t03B01
B:63-234
2b
RVT_1-1t03B02
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-1t03B03
B:317-419
3b
RVT_connect-1t03B04
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-1t03B05
B:238-307
4b
RVT_thumb-1t03B06
B:238-307
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Asym.Unit (260 KB)
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