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3L2V
Asym. Unit
Info
Asym.Unit (182 KB)
Biol.Unit 1 (342 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS (PFV) INTASOME IN COMPLEX WITH MANGANESE AND MK0518 (RALTEGRAVIR)
Authors
:
S. Hare, S. S. Gupta, P. Cherepanov
Date
:
15 Dec 09 (Deposition) - 09 Feb 10 (Release) - 16 Mar 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
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, Zinc, Dna-Binding, Zinc Binding, Hhcc Motif, Viral Protein, Recombination, Recombination-Dna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
S. Hare, S. S. Gupta, E. Valkov, A. Engelman, P. Cherepanov
Retroviral Intasome Assembly And Inhibition Of Dna Strand Transfer
Nature V. 464 232 2010
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Hetero Components
(5, 10)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
3a: AMMONIUM ION (NH4a)
4a: N-(4-FLUOROBENZYL)-5-HYDROXY-1-MET... (RLTa)
5a: ZINC ION (ZNa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
MN
3
Ligand/Ion
MANGANESE (II) ION
3
NH4
1
Ligand/Ion
AMMONIUM ION
4
RLT
1
Ligand/Ion
N-(4-FLUOROBENZYL)-5-HYDROXY-1-METHYL-2-(1-METHYL-1-{[(5-METHYL-1,3,4-OXADIAZOL-2-YL)CARBONYL]AMINO}ETHYL)-6-OXO-1,6-DIHYDROPYRIMIDINE-4-CARBOXAMIDE
5
ZN
1
Ligand/Ion
ZINC ION
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Sites
(10, 10)
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)
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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
ASP A:128 , ASP A:185 , RLT A:397
BINDING SITE FOR RESIDUE MN A 394
03
AC3
SOFTWARE
ASP A:128 , GLU A:221 , ASN A:224 , RLT A:397 , DA D:17
BINDING SITE FOR RESIDUE MN A 395
04
AC4
SOFTWARE
ASP B:128 , ASP B:185 , DA C:19
BINDING SITE FOR RESIDUE MN B 393
05
AC5
SOFTWARE
ASP A:116
BINDING SITE FOR RESIDUE NH4 A 396
06
AC6
SOFTWARE
ASP A:128 , ASP A:185 , GLN A:186 , TYR A:212 , PRO A:214 , GLU A:221 , MN A:394 , MN A:395 , DG C:4 , DC D:16 , DA D:17
BINDING SITE FOR RESIDUE RLT A 397
07
AC7
SOFTWARE
PRO A:135 , SER A:136 , GLN A:137 , LYS A:241
BINDING SITE FOR RESIDUE GOL A 801
08
AC8
SOFTWARE
HIS A:338 , LYS A:339 , HIS A:357
BINDING SITE FOR RESIDUE GOL A 802
09
AC9
SOFTWARE
SER A:162 , THR A:163 , SER A:164
BINDING SITE FOR RESIDUE GOL A 803
10
BC1
SOFTWARE
THR A:191 , PHE A:208
BINDING SITE FOR RESIDUE GOL A 804
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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_3l2vB01 (B:117-231)
1b: PFAM_rve_3l2vB02 (B:117-231)
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)
Clan
:
RNase_H
(288)
Family
:
rve
(46)
Human spumaretrovirus (SFVcpz(hu)) (Human foamy virus)
(26)
1a
rve-3l2vB01
B:117-231
1b
rve-3l2vB02
B:117-231
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Chain D
Asymmetric Unit 1
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Asym.Unit (182 KB)
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