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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3RF3
Asym. Unit
Info
Asym.Unit (394 KB)
Biol.Unit 1 (195 KB)
Biol.Unit 2 (196 KB)
Biol.Unit 3 (389 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
SHIGELLA IPAA-VBS3 IN COMPLEX WITH HUMAN VINCULIN
Authors
:
H. Park, A. Sharff, T. Izard
Date
:
05 Apr 11 (Deposition) - 27 Apr 11 (Release) - 23 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.61
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Alpha-Helix Bundle Domain, Cytoskeletal Protein, Protein-Protein Interactions, Cell Adhesion, Cytoskeleton, Bacterial Toxins, Pathogen-Host Interactions, Ipaa, Talin, F-Actin, Phosphatidylinositol 4 5-Bisphosphate, Cytosol, Focal Adhesion, Protein Binding-Toxin Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Park, C. Valencia-Gallardo, A. Sharff, G. Tran Van Nhieu, T. Izar
Novel Vinculin Binding Site Of The Ipaa Invasin Of Shigella
J. Biol. Chem. V. 286 23214 2011
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: CACODYLATE ION (CACa)
1b: CACODYLATE ION (CACb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CAC
2
Ligand/Ion
CACODYLATE ION
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:176 , LYS A:199 , HOH A:582 , HOH A:618
BINDING SITE FOR RESIDUE CAC A 300
2
AC2
SOFTWARE
ASP B:176 , LYS B:199 , HOH B:582 , HOH B:618
BINDING SITE FOR RESIDUE CAC B 300
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_037667 (V234L, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_037667
V
234
L
VINC_HUMAN
Polymorphism
17853882
A/B
V
234
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: VINCULIN_1 (A:162-182,B:162-182)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
VINCULIN_1
PS00663
Vinculin family talin-binding region signature.
VINC_HUMAN
162-182
2
A:162-182
B:162-182
[
close PROSITE info
]
Exons
(6, 12)
Info
All Exons
Exon 1.1a (A:2-56 | B:1-56)
Exon 1.2a (A:57-80 | B:57-80)
Exon 1.4 (A:80-130 | B:80-130)
Exon 1.5 (A:131-167 | B:131-167)
Exon 1.6 (A:167-208 | B:167-208)
Exon 1.7a (A:208-258 | B:208-258)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2a
3: Boundary 1.2a/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7a
7: Boundary 1.7a/1.8
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
1.1a
ENST00000211998
1a
ENSE00002146319
chr10:
75757872-75758133
262
VINC_HUMAN
1-56
56
2
A:2-56
B:1-56
55
56
1.2a
ENST00000211998
2a
ENSE00001607712
chr10:
75802841-75802911
71
VINC_HUMAN
57-80
24
2
A:57-80
B:57-80
24
24
1.4
ENST00000211998
4
ENSE00001024254
chr10:
75830428-75830578
151
VINC_HUMAN
80-130
51
2
A:80-130
B:80-130
51
51
1.5
ENST00000211998
5
ENSE00001024245
chr10:
75830733-75830841
109
VINC_HUMAN
131-167
37
2
A:131-167
B:131-167
37
37
1.6
ENST00000211998
6
ENSE00001024249
chr10:
75832488-75832610
123
VINC_HUMAN
167-208
42
2
A:167-208
B:167-208
42
42
1.7a
ENST00000211998
7a
ENSE00001024263
chr10:
75834501-75834661
161
VINC_HUMAN
208-261
54
2
A:208-258
B:208-258
51
51
1.8
ENST00000211998
8
ENSE00001024248
chr10:
75842212-75842302
91
VINC_HUMAN
262-292
31
0
-
-
1.9a
ENST00000211998
9a
ENSE00000986356
chr10:
75843124-75843271
148
VINC_HUMAN
292-341
50
0
-
-
1.10
ENST00000211998
10
ENSE00000986357
chr10:
75848954-75849107
154
VINC_HUMAN
341-392
52
0
-
-
1.11
ENST00000211998
11
ENSE00000986358
chr10:
75849781-75849956
176
VINC_HUMAN
393-451
59
0
-
-
1.12
ENST00000211998
12
ENSE00001024262
chr10:
75854029-75854219
191
VINC_HUMAN
451-515
65
0
-
-
1.13
ENST00000211998
13
ENSE00000986360
chr10:
75855414-75855613
200
VINC_HUMAN
515-581
67
0
-
-
1.14
ENST00000211998
14
ENSE00000986361
chr10:
75856962-75857090
129
VINC_HUMAN
582-624
43
0
-
-
1.15a
ENST00000211998
15a
ENSE00000986362
chr10:
75860706-75860855
150
VINC_HUMAN
625-674
50
0
-
-
1.16
ENST00000211998
16
ENSE00000986363
chr10:
75863578-75863686
109
VINC_HUMAN
675-711
37
0
-
-
1.17c
ENST00000211998
17c
ENSE00000986364
chr10:
75864809-75865111
303
VINC_HUMAN
711-812
102
0
-
-
1.18
ENST00000211998
18
ENSE00000986365
chr10:
75866988-75867112
125
VINC_HUMAN
812-853
42
0
-
-
1.19b
ENST00000211998
19b
ENSE00000834577
chr10:
75868729-75868914
186
VINC_HUMAN
854-915
62
0
-
-
1.20
ENST00000211998
20
ENSE00000709651
chr10:
75871667-75871870
204
VINC_HUMAN
916-983
68
0
-
-
1.21
ENST00000211998
21
ENSE00000709670
chr10:
75873942-75874145
204
VINC_HUMAN
984-1051
68
0
-
-
1.22
ENST00000211998
22
ENSE00000986366
chr10:
75874553-75874657
105
VINC_HUMAN
1052-1086
35
0
-
-
1.23a
ENST00000211998
23a
ENSE00001373600
chr10:
75877781-75879910
2130
VINC_HUMAN
1087-1134
48
0
-
-
[
close EXON info
]
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3rf3a1 (A:2-128)
1b: SCOP_d3rf3b1 (B:1-128)
1c: SCOP_d3rf3b2 (B:129-258)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
alpha-catenin/vinculin-like
(25)
Family
:
alpha-catenin/vinculin
(24)
Protein domain
:
automated matches
(8)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d3rf3a1
A:2-128
1b
d3rf3b1
B:1-128
1c
d3rf3b2
B:129-258
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_SipA_3rf3D01 (D:488-511)
1b: PFAM_SipA_3rf3D02 (D:488-511)
2a: PFAM_Vinculin_3rf3B01 (B:3-258)
2b: PFAM_Vinculin_3rf3B02 (B:3-258)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: SipA]
(1)
Family
:
SipA
(1)
Shigella flexneri
(1)
1a
SipA-3rf3D01
D:488-511
1b
SipA-3rf3D02
D:488-511
Clan
:
no clan defined [family: Vinculin]
(16)
Family
:
Vinculin
(16)
Homo sapiens (Human)
(8)
2a
Vinculin-3rf3B01
B:3-258
2b
Vinculin-3rf3B02
B:3-258
[
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 (394 KB)
Header - Asym.Unit
Biol.Unit 1 (195 KB)
Header - Biol.Unit 1
Biol.Unit 2 (196 KB)
Header - Biol.Unit 2
Biol.Unit 3 (389 KB)
Header - Biol.Unit 3
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
3RF3
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
