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.
2DM1
Asym. Unit
Info
Asym.Unit (357 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
Models
(20 )
Title
:
SOLUTION STRUCTURE OF THE SECOND SH3 DOMAIN OF HUMAN PROTEIN VAV-2
Authors
:
H. Endo, F. Hayashi, M. Yoshida, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
20 Apr 06 (Deposition) - 03 Apr 07 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A (20 x)
Keywords
:
Rho Family Guanine Nucleotide Exchange Factor, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Endo, F. Hayashi, M. Yoshida, S. Yokoyama
Solution Structure Of The Second Sh3 Domain Of Human Protein Vav-2
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: SH3 (-|A:8-66)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SH3
PS50002
Src homology 3 (SH3) domain profile.
VAV2_HUMAN
586-652
816-877
1
-
A:8-66
[
close PROSITE info
]
Exons
(3, 3)
Info
All Exons
Exon 1.32 (A:1-7)
Exon 1.33 (A:8-52)
Exon 1.34b (A:53-67)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.31/1.32
2: Boundary 1.32/1.33
3: Boundary 1.33/1.34b
4: Boundary 1.34b/-
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
1.1c
ENST00000371850
1c
ENSE00001894042
chr9:
136857432-136857197
236
VAV2_HUMAN
1-68
68
0
-
-
1.2b
ENST00000371850
2b
ENSE00001694493
chr9:
136804341-136804225
117
VAV2_HUMAN
69-107
39
0
-
-
1.6a
ENST00000371850
6a
ENSE00001134180
chr9:
136726554-136726496
59
VAV2_HUMAN
108-127
20
0
-
-
1.7
ENST00000371850
7
ENSE00001096267
chr9:
136699462-136699394
69
VAV2_HUMAN
127-150
24
0
-
-
1.8
ENST00000371850
8
ENSE00001051205
chr9:
136677338-136677236
103
VAV2_HUMAN
150-184
35
0
-
-
1.9
ENST00000371850
9
ENSE00001649860
chr9:
136675327-136675313
15
VAV2_HUMAN
185-189
5
0
-
-
1.10
ENST00000371850
10
ENSE00001051207
chr9:
136674260-136674162
99
VAV2_HUMAN
190-222
33
0
-
-
1.11
ENST00000371850
11
ENSE00001051214
chr9:
136672448-136672380
69
VAV2_HUMAN
223-245
23
0
-
-
1.12
ENST00000371850
12
ENSE00001051220
chr9:
136671303-136671203
101
VAV2_HUMAN
246-279
34
0
-
-
1.13
ENST00000371850
13
ENSE00001051196
chr9:
136662931-136662832
100
VAV2_HUMAN
279-312
34
0
-
-
1.14
ENST00000371850
14
ENSE00001051198
chr9:
136661646-136661551
96
VAV2_HUMAN
313-344
32
0
-
-
1.15
ENST00000371850
15
ENSE00001051199
chr9:
136660858-136660790
69
VAV2_HUMAN
345-367
23
0
-
-
1.16
ENST00000371850
16
ENSE00001134002
chr9:
136656991-136656905
87
VAV2_HUMAN
368-396
29
0
-
-
1.17
ENST00000371850
17
ENSE00001096253
chr9:
136654465-136654380
86
VAV2_HUMAN
397-425
29
0
-
-
1.18
ENST00000371850
18
ENSE00001096259
chr9:
136653608-136653476
133
VAV2_HUMAN
425-469
45
0
-
-
1.19
ENST00000371850
19
ENSE00001682200
chr9:
136652382-136652368
15
VAV2_HUMAN
470-474
5
0
-
-
1.20
ENST00000371850
20
ENSE00001096247
chr9:
136651007-136650898
110
VAV2_HUMAN
475-511
37
0
-
-
1.21
ENST00000371850
21
ENSE00001096246
chr9:
136649540-136649439
102
VAV2_HUMAN
511-545
35
0
-
-
1.22
ENST00000371850
22
ENSE00001133992
chr9:
136648713-136648625
89
VAV2_HUMAN
545-575
31
0
-
-
1.23
ENST00000371850
23
ENSE00001656614
chr9:
136645832-136645816
17
VAV2_HUMAN
575-580
6
0
-
-
1.25
ENST00000371850
25
ENSE00001388876
chr9:
136645061-136645040
22
VAV2_HUMAN
581-588
8
0
-
-
1.26
ENST00000371850
26
ENSE00001096262
chr9:
136644011-136643884
128
VAV2_HUMAN
588-630
43
0
-
-
1.27
ENST00000371850
27
ENSE00001133974
chr9:
136642585-136642511
75
VAV2_HUMAN
631-655
25
0
-
-
1.28
ENST00000371850
28
ENSE00001096269
chr9:
136641202-136641150
53
VAV2_HUMAN
656-673
18
0
-
-
1.29
ENST00000371850
29
ENSE00001096274
chr9:
136640173-136640057
117
VAV2_HUMAN
673-712
40
0
-
-
1.30
ENST00000371850
30
ENSE00001096237
chr9:
136637168-136637081
88
VAV2_HUMAN
712-741
30
0
-
-
1.31
ENST00000371850
31
ENSE00001096272
chr9:
136635623-136635500
124
VAV2_HUMAN
742-783
42
0
-
-
1.32
ENST00000371850
32
ENSE00001096231
chr9:
136634625-136634539
87
VAV2_HUMAN
783-812
30
1
A:1-7
7
1.33
ENST00000371850
33
ENSE00001096243
chr9:
136633718-136633564
155
VAV2_HUMAN
812-863
52
1
A:8-52
45
1.34b
ENST00000371850
34b
ENSE00001456304
chr9:
136629231-136627016
2216
VAV2_HUMAN
864-878
15
1
A:53-67
15
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2dm1a_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
SH3-like barrel
(1035)
Superfamily
:
SH3-domain
(369)
Family
:
automated matches
(114)
Protein domain
:
automated matches
(114)
Human (Homo sapiens) [TaxId: 9606]
(74)
1a
d2dm1a_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (357 KB)
Header - Asym.Unit
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
2DM1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help