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2DFK
Asym. Unit
Info
Asym.Unit (397 KB)
Biol.Unit 1 (198 KB)
Biol.Unit 2 (195 KB)
Biol.Unit 3 (388 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CDC42-COLLYBISTIN II COMPLEX
Authors
:
S. Xiang, E. Y. Kim, J. J. Connelly, N. Nassar, J. Kirsch, J. Winking, G. S H. Schindelin
Date
:
02 Mar 06 (Deposition) - 02 May 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Dh Domain, Ph Domain, Cell Cycle
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Xiang, E. Y. Kim, J. J. Connelly, N. Nassar, J. Kirsch, J. Winking, G. Schwarz, H. Schindelin
The Crystal Structure Of Cdc42 In Complex With Collybistin Ii, A Gephyrin-Interacting Guanine Nucleotide Exchange Factor.
J. Mol. Biol. V. 359 35 2006
[
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
6
Ligand/Ion
GLYCEROL
2
SO4
2
Ligand/Ion
SULFATE ION
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP D:11 , GLY D:12 , ALA D:13 , VAL D:14 , GLY D:15 , LYS D:16 , THR D:17 , ALA D:59 , HOH D:731 , HOH D:746 , HOH D:777
BINDING SITE FOR RESIDUE SO4 D 701
2
AC2
SOFTWARE
ASP B:11 , GLY B:12 , ALA B:13 , VAL B:14 , GLY B:15 , LYS B:16 , THR B:17 , GLU B:62 , HOH B:715 , HOH B:733
BINDING SITE FOR RESIDUE SO4 B 702
3
AC3
SOFTWARE
ARG A:104 , LYS D:153 , GLU D:171 , GLU D:178
BINDING SITE FOR RESIDUE GOL A 601
4
AC4
SOFTWARE
ARG A:215 , TYR A:216 , HOH A:769 , MET B:45 , GLY B:48
BINDING SITE FOR RESIDUE GOL A 602
5
AC5
SOFTWARE
SER B:22 , TYR B:23 , THR B:25 , ASN B:26 , GLN B:162
BINDING SITE FOR RESIDUE GOL B 603
6
AC6
SOFTWARE
THR D:24 , THR D:25
BINDING SITE FOR RESIDUE GOL D 604
7
AC7
SOFTWARE
THR D:24 , PHE D:37 , ASP D:38 , TYR D:40 , HOH D:784
BINDING SITE FOR RESIDUE GOL D 605
8
AC8
SOFTWARE
LYS A:115 , GLN A:116 , TYR A:117 , ASN A:118 , HOH A:655 , HOH A:660
BINDING SITE FOR RESIDUE GOL A 606
[
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]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_076337 (Y64C, 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
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: RHO (B:1-176,D:1-176)
2: DH_2 (A:50-234,C:50-234)
3: PH_DOMAIN (A:265-372,C:265-372)
;
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:1-176
2
DH_2
PS50010
Dbl homology (DH) domain profile.
ARHG9_RAT
110-294
2
A:50-234
C:50-234
3
PH_DOMAIN
PS50003
PH domain profile.
ARHG9_RAT
325-432
2
A:265-372
C:265-372
[
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Exons
(5, 10)
Info
All Exons
Exon 1.4 (B:1-35 | D:1-35)
Exon 1.6 (B:36-60 | D:36-60)
Exon 1.7 (B:60-96 | D:60-96)
Exon 1.8b (B:97-162 | D:97-162)
Exon 1.10a (B:163-191 (gaps) | D:163-191 (gaps...)
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:1-35
35
35
1.6
ENST00000400259
6
ENSE00000388403
chr1:
22408215-22408287
73
CDC42_HUMAN
36-60
25
2
B:36-60
D:36-60
25
25
1.7
ENST00000400259
7
ENSE00000759640
chr1:
22412932-22413041
110
CDC42_HUMAN
60-96
37
2
B:60-96
D:60-96
37
37
1.8b
ENST00000400259
8b
ENSE00000388405
chr1:
22413162-22413359
198
CDC42_HUMAN
97-162
66
2
B:97-162
D:97-162
66
66
1.10a
ENST00000400259
10a
ENSE00001357650
chr1:
22417921-22419416
1496
CDC42_HUMAN
163-191
29
2
B:163-191 (gaps)
D:163-191 (gaps)
29
29
[
close EXON info
]
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2dfka1 (A:37-239)
1b: SCOP_d2dfkc1 (C:45-239)
2a: SCOP_d2dfka2 (A:240-401)
2b: SCOP_d2dfkc2 (C:240-397)
3a: SCOP_d2dfkb_ (B:)
3b: SCOP_d2dfkd_ (D:)
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Protein Domains
(
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(
)
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
:
Rho guanine nucleotide exchange factor 9, Collybistin
(1)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(1)
1a
d2dfka1
A:37-239
1b
d2dfkc1
C:45-239
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
:
Rho guanine nucleotide exchange factor 9, Collybistin
(1)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(1)
2a
d2dfka2
A:240-401
2b
d2dfkc2
C:240-397
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
d2dfkb_
B:
3b
d2dfkd_
D:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2dfkD00 (D:-2-191)
1b: CATH_2dfkB00 (B:1-191)
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Architectures
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Topologies
(
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(
)
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)
Norway rat (Rattus norvegicus)
(38)
1a
2dfkD00
D:-2-191
1b
2dfkB00
B:1-191
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Chain C
Chain D
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Asym.Unit (397 KB)
Header - Asym.Unit
Biol.Unit 1 (198 KB)
Header - Biol.Unit 1
Biol.Unit 2 (195 KB)
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Biol.Unit 3 (388 KB)
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