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.
1KZG
Asym. Unit
Info
Asym.Unit (176 KB)
Biol.Unit 1 (89 KB)
Biol.Unit 2 (86 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
DBSCDC42(Y889F)
Authors
:
K. L. Rossman, D. K. Worthylake, J. T. Snyder, D. P. Siderovski, S. L. Campbell, J. Sondek
Date
:
06 Feb 02 (Deposition) - 20 Mar 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Guanine Nucleotide Exchange Factor, Small G-Protein, Cdc42, Dbs, Dh/Ph, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. L. Rossman, D. K. Worthylake, J. T. Snyder, D. P. Siderovski, S. L. Campbell, J. Sondek
A Crystallographic View Of Interactions Between Dbs And Cdc42: Ph Domain-Assisted Guanine Nucleotide Exchange.
Embo J. V. 21 1315 2002
(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
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_076337 (Y1064C, chain B/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_076337
Y
64
C
CDC42_HUMAN
Disease (TKS)
864309721
B
D
Y
64
1064
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 8)
Info
All PROSITE Patterns/Profiles
1: RHO (B:1-176,D:1001-1176)
2: DH_2 (A:632-812,C:1632-1812)
3: DH_1 (A:761-786,C:1761-1786)
4: PH_DOMAIN (A:830-946,C:1830-1946)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RHO
PS51420
small GTPase Rho family profile.
CDC42_HUMAN
1-176
2
B:1-176
D:1001-1176
2
DH_2
PS50010
Dbl homology (DH) domain profile.
MCF2L_MOUSE
632-812
2
A:632-812
C:1632-1812
3
DH_1
PS00741
Dbl homology (DH) domain signature.
MCF2L_MOUSE
761-786
2
A:761-786
C:1761-1786
4
PH_DOMAIN
PS50003
PH domain profile.
MCF2L_MOUSE
830-946
2
A:830-946
C:1830-1946
[
close PROSITE info
]
Exons
(5, 10)
Info
All Exons
Exon 1.4 (B:1-35 | D:1001-1035)
Exon 1.6 (B:36-60 | D:1036-1060)
Exon 1.7 (B:60-96 | D:1060-1096)
Exon 1.8b (B:97-162 | D:1097-1162)
Exon 1.10a (B:163-188 | D:1163-1177)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.4
2: Boundary 1.4/1.6
3: Boundary 1.6/1.7
4: Boundary 1.7/1.8b
5: Boundary 1.8b/1.10a
6: Boundary 1.10a/-
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
ENST00000400259
1a
ENSE00001132068
chr1:
22379120-22379235
116
CDC42_HUMAN
-
0
0
-
-
1.4
ENST00000400259
4
ENSE00002144782
chr1:
22404922-22405076
155
CDC42_HUMAN
1-35
35
2
B:1-35
D:1001-1035
35
35
1.6
ENST00000400259
6
ENSE00000388403
chr1:
22408215-22408287
73
CDC42_HUMAN
36-60
25
2
B:36-60
D:1036-1060
25
25
1.7
ENST00000400259
7
ENSE00000759640
chr1:
22412932-22413041
110
CDC42_HUMAN
60-96
37
2
B:60-96
D:1060-1096
37
37
1.8b
ENST00000400259
8b
ENSE00000388405
chr1:
22413162-22413359
198
CDC42_HUMAN
97-162
66
2
B:97-162
D:1097-1162
66
66
1.10a
ENST00000400259
10a
ENSE00001357650
chr1:
22417921-22419416
1496
CDC42_HUMAN
163-191
29
2
B:163-188
D:1163-1177
26
15
[
close EXON info
]
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1kzga1 (A:624-818)
1b: SCOP_d1kzgc1 (C:1624-1818)
2a: SCOP_d1kzga2 (A:819-965)
2b: SCOP_d1kzgc2 (C:1819-1960)
3a: SCOP_d1kzgb_ (B:)
3b: SCOP_d1kzgd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DBL homology domain (DH-domain)
(22)
Superfamily
:
DBL homology domain (DH-domain)
(22)
Family
:
DBL homology domain (DH-domain)
(19)
Protein domain
:
Dbl's big sister, Dbs
(4)
Mouse (Mus musculus) [TaxId: 10090]
(4)
1a
d1kzga1
A:624-818
1b
d1kzgc1
C:1624-1818
Class
:
All beta proteins
(24004)
Fold
:
PH domain-like barrel
(258)
Superfamily
:
PH domain-like
(257)
Family
:
Pleckstrin-homology domain (PH domain)
(102)
Protein domain
:
Dbl's big sister, Dbs
(4)
Mouse (Mus musculus) [TaxId: 10090]
(4)
2a
d1kzga2
A:819-965
2b
d1kzgc2
C:1819-1960
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
G proteins
(693)
Protein domain
:
CDC42
(28)
Human (Homo sapiens) [TaxId: 9606]
(27)
3a
d1kzgb_
B:
3b
d1kzgd_
D:
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1kzgB00 (B:1-188)
1b: CATH_1kzgD00 (D:1001-1177)
2a: CATH_1kzgA01 (A:624-816)
2b: CATH_1kzgC01 (C:1624-1816)
3a: CATH_1kzgC02 (C:1817-1960)
3b: CATH_1kzgA02 (A:817-965)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
House mouse (Mus musculus)
(47)
1a
1kzgB00
B:1-188
1b
1kzgD00
D:1001-1177
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Dbl Homology Domain; Chain A
(13)
Homologous Superfamily
:
Dbl Homology Domain; Chain A
(13)
House mouse (Mus musculus)
(7)
2a
1kzgA01
A:624-816
2b
1kzgC01
C:1624-1816
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
PH-domain like
(150)
Homologous Superfamily
:
Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
(147)
House mouse (Mus musculus)
(39)
3a
1kzgC02
C:1817-1960
3b
1kzgA02
A:817-965
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Ras_1kzgD01 (D:1005-1177)
1b: PFAM_Ras_1kzgD02 (D:1005-1177)
2a: PFAM_PH_1kzgC01 (C:1842-1946)
2b: PFAM_PH_1kzgC02 (C:1842-1946)
3a: PFAM_RhoGEF_1kzgC03 (C:1636-1811)
3b: PFAM_RhoGEF_1kzgC04 (C:1636-1811)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Homo sapiens (Human)
(141)
1a
Ras-1kzgD01
D:1005-1177
1b
Ras-1kzgD02
D:1005-1177
Clan
:
PH
(111)
Family
:
PH
(71)
Mus musculus (Mouse)
(20)
2a
PH-1kzgC01
C:1842-1946
2b
PH-1kzgC02
C:1842-1946
Clan
:
no clan defined [family: RhoGEF]
(22)
Family
:
RhoGEF
(22)
Mus musculus (Mouse)
(5)
3a
RhoGEF-1kzgC03
C:1636-1811
3b
RhoGEF-1kzgC04
C:1636-1811
[
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 (176 KB)
Header - Asym.Unit
Biol.Unit 1 (89 KB)
Header - Biol.Unit 1
Biol.Unit 2 (86 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
1KZG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
