PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2B4J
Asym. Unit
Info
Asym.Unit (83 KB)
Biol.Unit 1 (76 KB)
Biol.Unit 2 (150 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURAL BASIS FOR THE RECOGNITION BETWEEN HIV-1 INTEGRASE AND LEDGF/P75
Authors
:
P. Cherepanov, A. L. Ambrosio, S. Rahman, T. Ellenberger, A. Engelman
Date
:
24 Sep 05 (Deposition) - 25 Oct 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.02
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B,C,D (2x)
Keywords
:
Hiv, Integration, Transcription, Viral Protein, Recombination
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Cherepanov, A. L. Ambrosio, S. Rahman, T. Ellenberger, A. Engelman
Structural Basis For The Recognition Between Hiv-1 Integras And Transcriptional Coactivator P75
Proc. Natl. Acad. Sci. Usa V. 102 17308 2005
[
close entry info
]
Hetero Components
(2, 6)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
PO4
2
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:66 , HIS A:67 , LYS A:159 , LYS D:392
BINDING SITE FOR RESIDUE PO4 A 301
2
AC2
SOFTWARE
THR B:66 , HIS B:67 , LYS B:159 , LYS C:392
BINDING SITE FOR RESIDUE PO4 B 302
3
AC3
SOFTWARE
LEU C:352 , GLN C:353 , HIS C:356 , HIS C:393 , GLU C:395 , MET C:396
BINDING SITE FOR RESIDUE GOL C 443
4
AC4
SOFTWARE
HOH D:36 , LEU D:352 , GLN D:353 , HIS D:356 , HIS D:393 , GLU D:395 , MET D:396
BINDING SITE FOR RESIDUE GOL D 443
5
AC5
SOFTWARE
LYS B:71 , HIS B:171 , LEU B:172 , HOH B:454
BINDING SITE FOR RESIDUE GOL B 403
6
AC6
SOFTWARE
LYS A:71 , HIS A:171 , LEU A:172 , HOH A:448 , HOH A:458
BINDING SITE FOR RESIDUE GOL A 404
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(3, 6)
Info
All Exons
Exon 1.15 (C:346-368 | D:346-368)
Exon 1.16 (C:369-402 | D:369-402)
Exon 1.17 (C:403-426 | D:403-426)
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
2
C:346-368
D:346-368
23
23
1.16
ENST00000380738
16
ENSE00001132811
chr9:
15469056-15468955
102
PSIP1_HUMAN
369-402
34
2
C:369-402
D:369-402
34
34
1.17
ENST00000380738
17
ENSE00001132806
chr9:
15468841-15468628
214
PSIP1_HUMAN
403-474
72
2
C:403-426
D:403-426
24
24
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
-
-
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2b4jc1 (C:346-426)
1b: SCOP_d2b4jd_ (D:)
2a: SCOP_d2b4ja_ (A:)
2b: SCOP_d2b4jb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
N-cbl like
(37)
Superfamily
:
HIV integrase-binding domain
(4)
Family
:
HIV integrase-binding domain
(4)
Protein domain
:
PC4 and SFRS1-interacting protein, PSIP1
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2b4jc1
C:346-426
1b
d2b4jd_
D:
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
d2b4ja_
A:
2b
d2b4jb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2b4jB00 (B:57-208)
1b: CATH_2b4jA00 (A:56-208)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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.
(29)
1a
2b4jB00
B:57-208
1b
2b4jA00
A:56-208
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (83 KB)
Header - Asym.Unit
Biol.Unit 1 (76 KB)
Header - Biol.Unit 1
Biol.Unit 2 (150 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2B4J
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help