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3OYH
Asym. Unit
Info
Asym.Unit (117 KB)
Biol.Unit 1 (214 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS (PFV) INTASOME IN COMPLEX WITH MAGNESIUM AND THE INSTI MK0536
Authors
:
S. Hare, P. Cherepanov
Date
:
23 Sep 10 (Deposition) - 17 Nov 10 (Release) - 30 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.74
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (2x)
Keywords
:
Protein-Dna Complex, Tetramer, Dna Integration, Endonuclease, Metal- Binding, Multifunctional Enzyme, Nuclease, Nucleotidyltransferase, Nucleus, Transferase, Viral Nucleoprotein, Virion, Dna-Binding, Zinc Binding, Hhcc Motif, Viral Protein, Recombination, Inhibitor, Dna- Binding Protein-Dna Complex, Recombination, Viral Protein-Dna Complex
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Gene Ontology, PubMed, Web (Google)
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Reference
:
S. Hare, A. M. Vos, R. F. Clayton, J. W. Thuring, M. D. Cummings, P. Cherepanov
Molecular Mechanisms Of Retroviral Integrase Inhibition And The Evolution Of Viral Resistance.
Proc. Natl. Acad. Sci. Usa V. 107 20057 2010
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Hetero Components
(6, 12)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
3a: AMMONIUM ION (NH4a)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
5a: ZINC ION (ZNa)
6a: 6-(3-CHLORO-4-FLUOROBENZYL)-4-HYDR... (ZYNa)
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No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
MG
3
Ligand/Ion
MAGNESIUM ION
3
NH4
1
Ligand/Ion
AMMONIUM ION
4
SO4
2
Ligand/Ion
SULFATE ION
5
ZN
1
Ligand/Ion
ZINC ION
6
ZYN
1
Ligand/Ion
6-(3-CHLORO-4-FLUOROBENZYL)-4-HYDROXY-N,N-DIMETHYL-2-(1-METHYLETHYL)-3,5-DIOXO-2,3,5,6,7,8-HEXAHYDRO-2,6-NAPHTHYRIDINE-1-CARBOXAMIDE
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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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:62 , HIS A:66 , CYS A:96 , CYS A:99
BINDING SITE FOR RESIDUE ZN A 393
02
AC2
SOFTWARE
LYS B:219 , ARG B:222 , SER B:258 , PRO B:259 , VAL B:260
BINDING SITE FOR RESIDUE SO4 B 393
03
AC3
SOFTWARE
HIS A:338 , LYS A:339 , HIS A:357
BINDING SITE FOR RESIDUE SO4 A 394
04
AC4
SOFTWARE
SER A:162 , THR A:163 , SER A:164
BINDING SITE FOR RESIDUE GOL A 801
05
AC5
SOFTWARE
PRO A:135 , SER A:136 , GLN A:137 , LYS A:241
BINDING SITE FOR RESIDUE GOL A 802
06
AC6
SOFTWARE
GLN A:296 , TYR B:263 , GLN B:267 , ASP B:273
BINDING SITE FOR RESIDUE GOL A 803
07
AC7
SOFTWARE
GLN A:60 , TYR A:80 , PRO A:277 , PHE A:278
BINDING SITE FOR RESIDUE GOL A 805
08
AC8
SOFTWARE
ASP A:116
BINDING SITE FOR RESIDUE NH4 A 395
09
AC9
SOFTWARE
ASP A:128 , ASP A:185 , ZYN A:398
BINDING SITE FOR RESIDUE MG A 396
10
BC1
SOFTWARE
ASP A:128 , GLU A:221 , ASN A:224 , ZYN A:398
BINDING SITE FOR RESIDUE MG A 397
11
BC2
SOFTWARE
ASP B:128 , ASP B:185 , DA C:19
BINDING SITE FOR RESIDUE MG B 394
12
BC3
SOFTWARE
ASP A:128 , ASP A:185 , TYR A:212 , PRO A:214 , GLN A:215 , GLU A:221 , MG A:396 , MG A:397 , DG C:4 , DC D:16 , DA D:17
BINDING SITE FOR RESIDUE ZYN A 398
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: INTEGRASE (A:117-273,B:117-273)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTEGRASE
PS50994
Integrase catalytic domain profile.
POL_FOAMV
868-1024
2
A:117-273
B:117-273
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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CATH Domains
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all CATH domains
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_rve_3oyhB01 (B:117-231)
1b: PFAM_rve_3oyhB02 (B:117-231)
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Clans
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(
)
Clan
:
RNase_H
(288)
Family
:
rve
(46)
Human spumaretrovirus (SFVcpz(hu)) (Human foamy virus)
(26)
1a
rve-3oyhB01
B:117-231
1b
rve-3oyhB02
B:117-231
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Chain D
Asymmetric Unit 1
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Asym.Unit (117 KB)
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