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1N5Y
Asym. Unit
Info
Asym.Unit (256 KB)
Biol.Unit 1 (247 KB)
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(1)
Title
:
HIV-1 REVERSE TRANSCRIPTASE CROSSLINKED TO POST-TRANSLOCATION AZTMP-TERMINATED DNA (COMPLEX P)
Authors
:
S. G. Sarafianos, A. D. Clark Jr. , K. Das, S. Tuske, J. J. Birktoft, P. Ilankumaran, A. R. Ramesha, J. M. Sayer, D. M. Jerina, P. L. Boyer, S. H. Hughes, E. Arnold
Date
:
07 Nov 02 (Deposition) - 28 Jan 03 (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, Translocation, Nucleotide Excision, Drug Resistance, Complex P, Transferase/Immune System/Dna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. G. Sarafianos, A. D. Clark Jr. , K. Das, S. Tuske, J. J. Birktoft, P. Ilankumaran, A. R. Ramesha, J. M. Sayer, D. M. Jerina, P. L. Boyer, S. H. Hughes, E. Arnold
Structure Of Hiv-1 Reverse Transcriptase With Pre-Translocation And Post-Translocation Aztmp-Terminated Dna
Embo J. V. 21 6614 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONO... (ATMa)
2a: MAGNESIUM ION (MGa)
3a: N2-(3-MERCAPTOPROPYL)-2'-DEOXYGUAN... (MRGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATM
1
Mod. Nucleotide
3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2
MG
1
Ligand/Ion
MAGNESIUM ION
3
MRG
1
Mod. Nucleotide
N2-(3-MERCAPTOPROPYL)-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
[
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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 1001
[
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]
SAPs(SNPs)/Variants
(5, 6)
Info
(mutated residues are not available)
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:
Select:
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
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
(6, 7)
Info
All SCOP Domains
1a: SCOP_d1n5yh2 (H:124-225)
2a: SCOP_d1n5yl2 (L:108-211)
3a: SCOP_d1n5yh1 (H:1-123)
4a: SCOP_d1n5yl1 (L:1-107)
5a: SCOP_d1n5ya1 (A:430-558)
6a: SCOP_d1n5ya2 (A:1-429)
6b: SCOP_d1n5yb_ (B:)
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Classes
(
)
(
)
Folds
(
)
(
)
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
d1n5yh2
H:124-225
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Mouse (Mus musculus) [TaxId: 10090]
(345)
2a
d1n5yl2
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
d1n5yh1
H:1-123
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Mouse (Mus musculus), cluster 4 [TaxId: 10090]
(211)
4a
d1n5yl1
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
d1n5ya1
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
d1n5ya2
A:1-429
6b
d1n5yb_
B:
[
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]
CATH Domains
(4, 13)
Info
all CATH domains
1a: CATH_1n5yB02 (B:99-123,B:165-233)
1b: CATH_1n5yA02 (A:91-115,A:157-225)
1c: CATH_1n5yB03 (B:234-319)
1d: CATH_1n5yA03 (A:226-319)
1e: CATH_1n5yA04 (A:320-426)
1f: CATH_1n5yB04 (B:320-426)
2a: CATH_1n5yA05 (A:427-556)
3a: CATH_1n5yA01 (A:1-90,A:116-156)
3b: CATH_1n5yB01 (B:9-98,B:124-164)
4a: CATH_1n5yL02 (L:108-211)
4b: CATH_1n5yH01 (H:1-123)
4c: CATH_1n5yL01 (L:1-107)
4d: CATH_1n5yH02 (H:124-220)
View:
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(
)
(
)
Architectures
(
)
(
)
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
1n5yB02
B:99-123,B:165-233
1b
1n5yA02
A:91-115,A:157-225
1c
1n5yB03
B:234-319
1d
1n5yA03
A:226-319
1e
1n5yA04
A:320-426
1f
1n5yB04
B:320-426
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
[unclassified]
(102)
2a
1n5yA05
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
1n5yA01
A:1-90,A:116-156
3b
1n5yB01
B:9-98,B:124-164
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
[unclassified]
(54)
4a
1n5yL02
L:108-211
4b
1n5yH01
H:1-123
4c
1n5yL01
L:1-107
4d
1n5yH02
H:124-220
[
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]
Pfam Domains
(4, 7)
Info
all PFAM domains
1a: PFAM_RNase_H_1n5yA01 (A:435-557)
2a: PFAM_RVT_1_1n5yB01 (B:63-234)
2b: PFAM_RVT_1_1n5yB02 (B:63-234)
3a: PFAM_RVT_connect_1n5yB03 (B:317-419)
3b: PFAM_RVT_connect_1n5yB04 (B:317-419)
4a: PFAM_RVT_thumb_1n5yB05 (B:238-307)
4b: PFAM_RVT_thumb_1n5yB06 (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-1n5yA01
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_1-1n5yB01
B:63-234
2b
RVT_1-1n5yB02
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-1n5yB03
B:317-419
3b
RVT_connect-1n5yB04
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-1n5yB05
B:238-307
4b
RVT_thumb-1n5yB06
B:238-307
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Asym.Unit (256 KB)
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