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1K6Y
Biol. Unit 2
Info
Asym.Unit (130 KB)
Biol.Unit 1 (124 KB)
Biol.Unit 2 (125 KB)
Biol.Unit 3 (64 KB)
Biol.Unit 4 (64 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A TWO-DOMAIN FRAGMENT OF HIV-1 INTEGRASE
Authors
:
J. Wang, H. Ling, W. Yang, R. Craigie
Date
:
17 Oct 01 (Deposition) - 21 Dec 01 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B,C,D (1x)
Biol. Unit 3: A,B (1x)
Biol. Unit 4: C,D (1x)
Keywords
:
Hiv-1, Integrase, Domain Organization, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Y. Wang, H. Ling, W. Yang, R. Craigie
Structure Of A Two-Domain Fragment Of Hiv-1 Integrase: Implications For Domain Organization In The Intact Protein.
Embo J. V. 20 7333 2001
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
PO4
2
Ligand/Ion
PHOSPHATE ION
3
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(12, 12)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:12 , HIS A:16 , CYS A:40 , CYS A:43
BINDING SITE FOR RESIDUE ZN A 401
02
AC2
SOFTWARE
HIS B:12 , HIS B:16 , CYS B:40 , CYS B:43
BINDING SITE FOR RESIDUE ZN B 402
03
AC3
SOFTWARE
HIS C:12 , HIS C:16 , CYS C:40 , CYS C:43
BINDING SITE FOR RESIDUE ZN C 403
04
AC4
SOFTWARE
HIS D:12 , HIS D:16 , CYS D:40 , CYS D:43
BINDING SITE FOR RESIDUE ZN D 404
05
AC5
SOFTWARE
VAL A:37 , ALA A:38 , CYS A:40 , CYS A:43
BINDING SITE FOR RESIDUE K A 451
06
AC6
SOFTWARE
VAL B:37 , ALA B:38 , CYS B:40 , CYS B:43
BINDING SITE FOR RESIDUE K B 452
07
AC7
SOFTWARE
VAL C:37 , ALA C:38 , CYS C:40 , CYS C:43
BINDING SITE FOR RESIDUE K C 453
08
AC8
SOFTWARE
VAL D:37 , ALA D:38 , CYS D:40 , CYS D:43
BINDING SITE FOR RESIDUE K D 454
09
AC9
SOFTWARE
CYS A:65 , THR A:66 , HIS A:67 , ASN A:155 , LYS A:159 , HIS D:171
BINDING SITE FOR RESIDUE PO4 A 501
10
BC1
SOFTWARE
THR B:66 , HIS B:67 , SER B:119
BINDING SITE FOR RESIDUE PO4 B 502
11
BC2
SOFTWARE
THR C:66 , HIS C:67 , LYS C:159
BINDING SITE FOR RESIDUE PO4 C 503
12
BC3
SOFTWARE
THR D:66 , HIS D:67 , LYS D:159
BINDING SITE FOR RESIDUE PO4 D 504
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ZF_INTEGRASE (A:3-44,B:3-44,C:3-44,D:3-44)
2: INTEGRASE (A:56-204,B:56-204,C:56-204,D:56-20...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZF_INTEGRASE
PS50876
Zinc finger integrase-type profile.
POL_HV1N5
1150-1191
4
A:3-44
B:3-44
C:3-44
D:3-44
2
INTEGRASE
PS50994
Integrase catalytic domain profile.
POL_HV1N5
1201-1351
4
A:56-204
B:56-204
C:56-204
D:56-204
[
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Exons
(0, 0)
Info
All Exons
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1k6ya1 (A:1-46)
1b: SCOP_d1k6yb1 (B:1-46)
1c: SCOP_d1k6yc1 (C:1-46)
1d: SCOP_d1k6yd1 (D:1-46)
2a: SCOP_d1k6ya2 (A:56-210)
2b: SCOP_d1k6yb2 (B:56-212)
2c: SCOP_d1k6yc2 (C:56-209)
2d: SCOP_d1k6yd2 (D:56-211)
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Classes
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)
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)
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)
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
N-terminal Zn binding domain of HIV integrase
(8)
Family
:
N-terminal Zn binding domain of HIV integrase
(8)
Protein domain
:
N-terminal Zn binding domain of HIV integrase
(8)
Human immunodeficiency virus type 1 [TaxId: 11676]
(7)
1a
d1k6ya1
A:1-46
1b
d1k6yb1
B:1-46
1c
d1k6yc1
C:1-46
1d
d1k6yd1
D:1-46
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
Retroviral integrase, catalytic domain
(152)
Protein domain
:
Retroviral integrase, catalytic domain
(62)
Human immunodeficiency virus type 1 [TaxId: 11676]
(38)
2a
d1k6ya2
A:56-210
2b
d1k6yb2
B:56-212
2c
d1k6yc2
C:56-209
2d
d1k6yd2
D:56-211
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1k6yB02 (B:56-212)
1b: CATH_1k6yA02 (A:56-210)
1c: CATH_1k6yC02 (C:56-209)
1d: CATH_1k6yD02 (D:56-211)
2a: CATH_1k6yA01 (A:1-46)
2b: CATH_1k6yB01 (B:1-46)
2c: CATH_1k6yC01 (C:1-46)
2d: CATH_1k6yD01 (D:1-46)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
Human immunodeficiency virus 1. Organism_taxid: 11676.
(17)
1a
1k6yB02
B:56-212
1b
1k6yA02
A:56-210
1c
1k6yC02
C:56-209
1d
1k6yD02
D:56-211
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
[code=1.10.10.200, no name defined]
(11)
Human immunodeficiency virus 1. Organism_taxid: 11676.
(1)
2a
1k6yA01
A:1-46
2b
1k6yB01
B:1-46
2c
1k6yC01
C:1-46
2d
1k6yD01
D:1-46
[
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]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_rve_1k6yD01 (D:56-162)
1b: PFAM_rve_1k6yD02 (D:56-162)
1c: PFAM_rve_1k6yD03 (D:56-162)
1d: PFAM_rve_1k6yD04 (D:56-162)
2a: PFAM_Integrase_Zn_1k6yD05 (D:8-46)
2b: PFAM_Integrase_Zn_1k6yD06 (D:8-46)
2c: PFAM_Integrase_Zn_1k6yD07 (D:8-46)
2d: PFAM_Integrase_Zn_1k6yD08 (D:8-46)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
RNase_H
(288)
Family
:
rve
(46)
Human immunodeficiency virus 1
(6)
1a
rve-1k6yD01
D:56-162
1b
rve-1k6yD02
D:56-162
1c
rve-1k6yD03
D:56-162
1d
rve-1k6yD04
D:56-162
Clan
:
no clan defined [family: Integrase_Zn]
(7)
Family
:
Integrase_Zn
(7)
Human immunodeficiency virus 1
(1)
2a
Integrase_Zn-1k6yD05
D:8-46
2b
Integrase_Zn-1k6yD06
D:8-46
2c
Integrase_Zn-1k6yD07
D:8-46
2d
Integrase_Zn-1k6yD08
D:8-46
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