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3F9K
Asym. Unit
Info
Asym.Unit (949 KB)
Biol.Unit 1 (89 KB)
Biol.Unit 10 (90 KB)
Biol.Unit 11 (89 KB)
Biol.Unit 12 (90 KB)
Biol.Unit 13 (244 KB)
Biol.Unit 14 (242 KB)
Biol.Unit 15 (243 KB)
Biol.Unit 16 (244 KB)
Biol.Unit 2 (90 KB)
Biol.Unit 3 (89 KB)
Biol.Unit 4 (90 KB)
Biol.Unit 5 (89 KB)
Biol.Unit 6 (89 KB)
Biol.Unit 7 (89 KB)
Biol.Unit 8 (90 KB)
Biol.Unit 9 (90 KB)
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Title
:
TWO DOMAIN FRAGMENT OF HIV-2 INTEGRASE IN COMPLEX WITH LEDGF IBD
Authors
:
S. Hare, P. Cherepanov
Date
:
14 Nov 08 (Deposition) - 20 Jan 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,E,F,G,I,J,K,M,N,O,Q,R,S,U,V,W,Y,Z,a,c,d,e,g,h,i,k,l,m,o,p,q,s,t,u
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: E,F,G (1x)
Biol. Unit 3: I,J,K (1x)
Biol. Unit 4: M,N,O (1x)
Biol. Unit 5: Q,R,S (1x)
Biol. Unit 6: U,V,W (1x)
Biol. Unit 7: Y,Z,a (1x)
Biol. Unit 8: c,d,e (1x)
Biol. Unit 9: g,h,i (1x)
Biol. Unit 10: k,l,m (1x)
Biol. Unit 11: o,p,q (1x)
Biol. Unit 12: s,t,u (1x)
Biol. Unit 13: E,F,G,U,V,W,g,h,i (1x)
Biol. Unit 14: A,B,C,I,J,K,Y,Z,a (1x)
Biol. Unit 15: k,l,m,o,p,q,s,t,u (1x)
Biol. Unit 16: M,N,O,Q,R,S,c,d,e (1x)
Keywords
:
Protein-Protein Complex, Aids, Dna Integration, Endonuclease, Magnesium, Metal-Binding, Multifunctional Enzyme, Nuclease, Nucleotidyltransferase, Nucleus, Transferase, Viral Nucleoprotein, Virion, Dna-Binding, Host-Virus Interaction, Transcription, Transcription Regulation, Zinc Binding, Hhcc Motif, Viral Protein, Recombination
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Hare, M. C. Shun, S. S. Gupta, E. Valkov, A. Engelman, P. Cherepanov
A Novel Co-Crystal Structure Affords The Design Of Gain-Of-Function Lentiviral Integrase Mutants In The Presence Of Modified Psip1/Ledgf/P75
Plos Pathog. V. 5 E1000 2009
[
close entry info
]
Hetero Components
(2, 48)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
1i: MAGNESIUM ION (MGi)
1j: MAGNESIUM ION (MGj)
1k: MAGNESIUM ION (MGk)
1l: MAGNESIUM ION (MGl)
1m: MAGNESIUM ION (MGm)
1n: MAGNESIUM ION (MGn)
1o: MAGNESIUM ION (MGo)
1p: MAGNESIUM ION (MGp)
1q: MAGNESIUM ION (MGq)
1r: MAGNESIUM ION (MGr)
1s: MAGNESIUM ION (MGs)
1t: MAGNESIUM ION (MGt)
1u: MAGNESIUM ION (MGu)
1v: MAGNESIUM ION (MGv)
1w: MAGNESIUM ION (MGw)
1x: MAGNESIUM ION (MGx)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
2i: ZINC ION (ZNi)
2j: ZINC ION (ZNj)
2k: ZINC ION (ZNk)
2l: ZINC ION (ZNl)
2m: ZINC ION (ZNm)
2n: ZINC ION (ZNn)
2o: ZINC ION (ZNo)
2p: ZINC ION (ZNp)
2q: ZINC ION (ZNq)
2r: ZINC ION (ZNr)
2s: ZINC ION (ZNs)
2t: ZINC ION (ZNt)
2u: ZINC ION (ZNu)
2v: ZINC ION (ZNv)
2w: ZINC ION (ZNw)
2x: ZINC ION (ZNx)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
24
Ligand/Ion
MAGNESIUM ION
2
ZN
24
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(48, 48)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
View:
Select:
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 210
02
AC2
SOFTWARE
ASP A:64 , ASP A:116
BINDING SITE FOR RESIDUE MG A 211
03
AC3
SOFTWARE
HIS B:12 , HIS B:16 , CYS B:40 , CYS B:43
BINDING SITE FOR RESIDUE ZN B 210
04
AC4
SOFTWARE
ASP B:64 , ASP B:116 , GLU e:375
BINDING SITE FOR RESIDUE MG B 211
05
AC5
SOFTWARE
HIS E:12 , HIS E:16 , CYS E:40 , CYS E:43
BINDING SITE FOR RESIDUE ZN E 210
06
AC6
SOFTWARE
ASP E:64 , ASP E:116
BINDING SITE FOR RESIDUE MG E 211
07
AC7
SOFTWARE
HIS F:12 , HIS F:16 , CYS F:40 , CYS F:43
BINDING SITE FOR RESIDUE ZN F 210
08
AC8
SOFTWARE
ASP F:64 , ASP F:116
BINDING SITE FOR RESIDUE MG F 211
09
AC9
SOFTWARE
HIS I:12 , HIS I:16 , CYS I:40 , CYS I:43
BINDING SITE FOR RESIDUE ZN I 210
10
BC1
SOFTWARE
ASP I:64 , ASP I:116
BINDING SITE FOR RESIDUE MG I 211
11
BC2
SOFTWARE
HIS J:12 , HIS J:16 , CYS J:40 , CYS J:43
BINDING SITE FOR RESIDUE ZN J 210
12
BC3
SOFTWARE
ASP J:64 , ASP J:116 , GLU W:375
BINDING SITE FOR RESIDUE MG J 211
13
BC4
SOFTWARE
HIS M:12 , HIS M:16 , CYS M:40 , CYS M:43
BINDING SITE FOR RESIDUE ZN M 210
14
BC5
SOFTWARE
ASP M:64 , ASP M:116
BINDING SITE FOR RESIDUE MG M 211
15
BC6
SOFTWARE
HIS N:12 , HIS N:16 , CYS N:40 , CYS N:43
BINDING SITE FOR RESIDUE ZN N 210
16
BC7
SOFTWARE
GLU G:375 , ASP N:64 , CYS N:65 , ASP N:116
BINDING SITE FOR RESIDUE MG N 211
17
BC8
SOFTWARE
HIS Q:12 , HIS Q:16 , CYS Q:40 , CYS Q:43
BINDING SITE FOR RESIDUE ZN Q 210
18
BC9
SOFTWARE
ASP Q:64 , ASP Q:116
BINDING SITE FOR RESIDUE MG Q 211
19
CC1
SOFTWARE
HIS R:12 , HIS R:16 , CYS R:40 , CYS R:43
BINDING SITE FOR RESIDUE ZN R 210
20
CC2
SOFTWARE
ASP R:64 , ASP R:116
BINDING SITE FOR RESIDUE MG R 211
21
CC3
SOFTWARE
HIS U:12 , HIS U:16 , CYS U:40 , CYS U:43
BINDING SITE FOR RESIDUE ZN U 210
22
CC4
SOFTWARE
ASP U:64 , ASP U:116
BINDING SITE FOR RESIDUE MG U 211
23
CC5
SOFTWARE
HIS V:12 , HIS V:16 , CYS V:40 , CYS V:43
BINDING SITE FOR RESIDUE ZN V 210
24
CC6
SOFTWARE
ASP V:64 , ASP V:116
BINDING SITE FOR RESIDUE MG V 211
25
CC7
SOFTWARE
HIS Y:12 , HIS Y:16 , CYS Y:40 , CYS Y:43
BINDING SITE FOR RESIDUE ZN Y 210
26
CC8
SOFTWARE
ASP Y:64 , ASP Y:116
BINDING SITE FOR RESIDUE MG Y 211
27
CC9
SOFTWARE
HIS Z:12 , HIS Z:16 , CYS Z:40 , CYS Z:43
BINDING SITE FOR RESIDUE ZN Z 210
28
DC1
SOFTWARE
ASP Z:64 , ASP Z:116
BINDING SITE FOR RESIDUE MG Z 211
29
DC2
SOFTWARE
HIS c:12 , HIS c:16 , CYS c:40 , CYS c:43
BINDING SITE FOR RESIDUE ZN c 210
30
DC3
SOFTWARE
ASP c:64 , ASP c:116
BINDING SITE FOR RESIDUE MG c 211
31
DC4
SOFTWARE
HIS d:12 , HIS d:16 , CYS d:40 , CYS d:43
BINDING SITE FOR RESIDUE ZN d 210
32
DC5
SOFTWARE
ASP d:64 , ASP d:116
BINDING SITE FOR RESIDUE MG d 211
33
DC6
SOFTWARE
HIS g:12 , HIS g:16 , CYS g:40 , CYS g:43
BINDING SITE FOR RESIDUE ZN g 210
34
DC7
SOFTWARE
ASP g:64 , ASP g:116
BINDING SITE FOR RESIDUE MG g 211
35
DC8
SOFTWARE
HIS h:12 , HIS h:16 , CYS h:40 , CYS h:43
BINDING SITE FOR RESIDUE ZN h 210
36
DC9
SOFTWARE
ASP h:64 , ASP h:116
BINDING SITE FOR RESIDUE MG h 211
37
EC1
SOFTWARE
HIS k:12 , HIS k:16 , CYS k:40 , CYS k:43
BINDING SITE FOR RESIDUE ZN k 210
38
EC2
SOFTWARE
ASP k:64 , ASP k:116
BINDING SITE FOR RESIDUE MG k 211
39
EC3
SOFTWARE
HIS l:12 , HIS l:16 , CYS l:40 , CYS l:43
BINDING SITE FOR RESIDUE ZN l 210
40
EC4
SOFTWARE
GLU S:375 , ASP l:64 , ASP l:116
BINDING SITE FOR RESIDUE MG l 211
41
EC5
SOFTWARE
HIS o:12 , HIS o:16 , CYS o:40 , CYS o:43
BINDING SITE FOR RESIDUE ZN o 210
42
EC6
SOFTWARE
ASP o:64 , ASP o:116
BINDING SITE FOR RESIDUE MG o 211
43
EC7
SOFTWARE
HIS p:12 , HIS p:16 , CYS p:40 , CYS p:43
BINDING SITE FOR RESIDUE ZN p 210
44
EC8
SOFTWARE
ASP p:64 , ASP p:116
BINDING SITE FOR RESIDUE MG p 211
45
EC9
SOFTWARE
HIS s:12 , HIS s:16 , CYS s:40 , CYS s:43
BINDING SITE FOR RESIDUE ZN s 210
46
FC1
SOFTWARE
ASP s:64 , ASP s:116
BINDING SITE FOR RESIDUE MG s 211
47
FC2
SOFTWARE
HIS t:12 , HIS t:16 , CYS t:40 , CYS t:43
BINDING SITE FOR RESIDUE ZN t 210
48
FC3
SOFTWARE
ASP t:64 , ASP t:116
BINDING SITE FOR RESIDUE MG t 211
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 36)
Info
All PROSITE Patterns/Profiles
1: ZF_INTEGRASE (B:3-43,F:3-43,J:3-43,N:3-43,R:3-43...)
2: INTEGRASE (A:53-204,B:54-204,E:53-204,F:54-20...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZF_INTEGRASE
PS50876
Zinc finger integrase-type profile.
POL_HV2RO
1174-1215
12
B:3-43
F:3-43
J:3-43
N:3-43
R:3-43
V:3-43
Z:3-43
d:3-43
h:3-43
l:3-43
p:3-43
t:3-43
2
INTEGRASE
PS50994
Integrase catalytic domain profile.
POL_HV2RO
1224-1375
24
A:53-204
B:54-204
E:53-204
F:54-204
I:53-204
J:54-204
M:53-204
N:54-204
Q:53-204
R:54-204
U:53-204
V:54-204
Y:53-204
Z:54-204
c:53-204
d:54-204
g:53-204
h:54-204
k:53-204
l:54-204
o:53-204
p:54-204
s:53-204
t:54-204
[
close PROSITE info
]
Exons
(3, 36)
Info
All Exons
Exon 1.15 (C:347-368 | G:347-368 | K:347-368 ...)
Exon 1.16 (C:369-402 | G:369-402 | K:369-402 ...)
Exon 1.17 (C:403-440 | G:403-440 | K:403-440 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.14/1.15
2: Boundary 1.15/1.16
3: Boundary 1.16/1.17
4: Boundary 1.17/1.18
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000380738
1b
ENSE00001871552
chr9:
15510993-15510815
179
PSIP1_HUMAN
-
0
0
-
-
1.2b
ENST00000380738
2b
ENSE00002140211
chr9:
15510324-15510115
210
PSIP1_HUMAN
1-24
24
0
-
-
1.3a
ENST00000380738
3a
ENSE00001132884
chr9:
15506635-15506559
77
PSIP1_HUMAN
25-50
26
0
-
-
1.5
ENST00000380738
5
ENSE00001132876
chr9:
15490122-15489984
139
PSIP1_HUMAN
50-96
47
0
-
-
1.7
ENST00000380738
7
ENSE00001089135
chr9:
15486929-15486825
105
PSIP1_HUMAN
97-131
35
0
-
-
1.8b
ENST00000380738
8b
ENSE00001132860
chr9:
15486066-15486004
63
PSIP1_HUMAN
132-152
21
0
-
-
1.9
ENST00000380738
9
ENSE00001132852
chr9:
15479685-15479589
97
PSIP1_HUMAN
153-185
33
0
-
-
1.10
ENST00000380738
10
ENSE00001132844
chr9:
15478550-15478475
76
PSIP1_HUMAN
185-210
26
0
-
-
1.11a
ENST00000380738
11a
ENSE00001132838
chr9:
15474235-15474007
229
PSIP1_HUMAN
210-286
77
0
-
-
1.12a
ENST00000380738
12a
ENSE00001420149
chr9:
15472748-15472630
119
PSIP1_HUMAN
287-326
40
0
-
-
1.14
ENST00000380738
14
ENSE00001132824
chr9:
15469991-15469936
56
PSIP1_HUMAN
326-345
20
0
-
-
1.15
ENST00000380738
15
ENSE00001132819
chr9:
15469334-15469264
71
PSIP1_HUMAN
345-368
24
12
C:347-368
G:347-368
K:347-368
O:347-368
S:347-368
W:347-368
a:347-368
e:347-368
i:347-368
m:347-368
q:347-368
u:347-368
22
22
22
22
22
22
22
22
22
22
22
22
1.16
ENST00000380738
16
ENSE00001132811
chr9:
15469056-15468955
102
PSIP1_HUMAN
369-402
34
12
C:369-402
G:369-402
K:369-402
O:369-402
S:369-402
W:369-402
a:369-402
e:369-402
i:369-402
m:369-402
q:369-402
u:369-402
34
34
34
34
34
34
34
34
34
34
34
34
1.17
ENST00000380738
17
ENSE00001132806
chr9:
15468841-15468628
214
PSIP1_HUMAN
403-474
72
12
C:403-440
G:403-440
K:403-440
O:403-440
S:403-440
W:403-440
a:403-440
e:403-440
i:403-440
m:403-440
q:403-440
u:403-440
38
38
38
38
38
38
38
38
38
38
38
38
1.18
ENST00000380738
18
ENSE00001089131
chr9:
15466857-15466746
112
PSIP1_HUMAN
474-511
38
0
-
-
1.19
ENST00000380738
19
ENSE00001486085
chr9:
15465578-15464064
1515
PSIP1_HUMAN
511-530
20
0
-
-
[
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SCOP Domains
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All SCOP Domains
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CATH Domains
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all CATH domains
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Pfam Domains
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all PFAM domains
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Asym.Unit (949 KB)
Header - Asym.Unit
Biol.Unit 1 (89 KB)
Header - Biol.Unit 1
Biol.Unit 10 (90 KB)
Header - Biol.Unit 10
Biol.Unit 11 (89 KB)
Header - Biol.Unit 11
Biol.Unit 12 (90 KB)
Header - Biol.Unit 12
Biol.Unit 13 (244 KB)
Header - Biol.Unit 13
Biol.Unit 14 (242 KB)
Header - Biol.Unit 14
Biol.Unit 15 (243 KB)
Header - Biol.Unit 15
Biol.Unit 16 (244 KB)
Header - Biol.Unit 16
Biol.Unit 2 (90 KB)
Header - Biol.Unit 2
Biol.Unit 3 (89 KB)
Header - Biol.Unit 3
Biol.Unit 4 (90 KB)
Header - Biol.Unit 4
Biol.Unit 5 (89 KB)
Header - Biol.Unit 5
Biol.Unit 6 (89 KB)
Header - Biol.Unit 6
Biol.Unit 7 (89 KB)
Header - Biol.Unit 7
Biol.Unit 8 (90 KB)
Header - Biol.Unit 8
Biol.Unit 9 (90 KB)
Header - Biol.Unit 9
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