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2NGR
Asym. Unit
Info
Asym.Unit (71 KB)
Biol.Unit 1 (66 KB)
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(1)
Title
:
TRANSITION STATE COMPLEX FOR GTP HYDROLYSIS BY CDC42: COMPARISONS OF THE HIGH RESOLUTION STRUCTURES FOR CDC42 BOUND TO THE ACTIVE AND CATALYTICALLY COMPROMISED FORMS OF THE CDC42-GAP.
Authors
:
N. Nassar, G. Hoffman, J. Clardy, R. Cerione
Date
:
31 Jul 98 (Deposition) - 06 Jan 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Transition State, G-Protein, Gap, Cdc42, Alf3. , Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Nassar, G. R. Hoffman, D. Manor, J. C. Clardy, R. A. Cerione
Structures Of Cdc42 Bound To The Active And Catalytically Compromised Forms Of Cdc42Gap.
Nat. Struct. Biol. V. 5 1047 1998
(for further references see the
PDB file header
)
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: ALUMINUM FLUORIDE (AF3a)
2a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
3a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AF3
1
Ligand/Ion
ALUMINUM FLUORIDE
2
GDP
1
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
3
MG
1
Ligand/Ion
MAGNESIUM ION
[
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:17 , THR A:35 , GDP A:198 , AF3 A:200 , HOH A:517 , HOH A:534
BINDING SITE FOR RESIDUE MG A 199
2
AC2
SOFTWARE
ALA A:13 , VAL A:14 , GLY A:15 , LYS A:16 , THR A:17 , CYS A:18 , PHE A:28 , TYR A:32 , GLN A:116 , ASP A:118 , LEU A:119 , SER A:158 , ALA A:159 , LEU A:160 , MG A:199 , AF3 A:200 , HOH A:517 , HOH A:533 , HOH A:534
BINDING SITE FOR RESIDUE GDP A 198
3
AC3
SOFTWARE
GLY A:12 , ALA A:13 , LYS A:16 , TYR A:32 , PRO A:34 , THR A:35 , GLY A:60 , GLN A:61 , GDP A:198 , MG A:199 , HOH A:509 , HOH A:517 , HOH A:534
BINDING SITE FOR RESIDUE AF3 A 200
[
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_049137 (R392C, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_049137
R
369
C
RHG01_HUMAN
Polymorphism
11822837
B
R
392
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: RHO (A:1-176)
2: RHOGAP (B:267-454)
;
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
1
A:1-176
2
RHOGAP
PS50238
Rho GTPase-activating proteins domain profile.
RHG01_HUMAN
244-431
1
B:267-454
[
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Exons
(11, 11)
Info
All Exons
Exon 1.9 (B:260-271)
Exon 1.10 (B:271-297)
Exon 1.11 (B:297-323)
Exon 1.12b (B:323-366)
Exon 1.13 (B:366-400)
Exon 1.14d (B:401-455)
Exon 2.4 (A:1-35)
Exon 2.6 (A:36-60)
Exon 2.7 (A:60-96)
Exon 2.8b (A:97-162)
Exon 2.10a (A:163-191)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.8b/1.9
02: Boundary 1.9/1.10
03: Boundary 1.10/1.11
04: Boundary 1.11/1.12b
05: Boundary 1.12b/1.13
06: Boundary 1.13/1.14d
07: Boundary 1.14d/-
08: Boundary 2.1a/2.4
09: Boundary 2.4/2.6
10: Boundary 2.6/2.7
11: Boundary 2.7/2.8b
12: Boundary 2.8b/2.10a
13: Boundary 2.10a/-
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
1.1c
ENST00000311956
1c
ENSE00002153911
chr11:
46722149-46722101
49
RHG01_HUMAN
-
0
0
-
-
1.3a
ENST00000311956
3a
ENSE00002177295
chr11:
46717706-46717525
182
RHG01_HUMAN
1-45
45
0
-
-
1.4a
ENST00000311956
4a
ENSE00001228762
chr11:
46717305-46717210
96
RHG01_HUMAN
45-77
33
0
-
-
1.5a
ENST00000311956
5a
ENSE00001228757
chr11:
46709810-46709723
88
RHG01_HUMAN
77-106
30
0
-
-
1.6
ENST00000311956
6
ENSE00001181605
chr11:
46703732-46703601
132
RHG01_HUMAN
106-150
45
0
-
-
1.7b
ENST00000311956
7b
ENSE00001181598
chr11:
46702929-46702843
87
RHG01_HUMAN
150-179
30
0
-
-
1.8b
ENST00000311956
8b
ENSE00001181594
chr11:
46702659-46702561
99
RHG01_HUMAN
179-212
34
0
-
-
1.9
ENST00000311956
9
ENSE00001181590
chr11:
46702297-46702190
108
RHG01_HUMAN
212-248
37
1
B:260-271
12
1.10
ENST00000311956
10
ENSE00001181585
chr11:
46702113-46702037
77
RHG01_HUMAN
248-274
27
1
B:271-297
27
1.11
ENST00000311956
11
ENSE00001181582
chr11:
46701832-46701755
78
RHG01_HUMAN
274-300
27
1
B:297-323
27
1.12b
ENST00000311956
12b
ENSE00001181578
chr11:
46701326-46701198
129
RHG01_HUMAN
300-343
44
1
B:323-366
44
1.13
ENST00000311956
13
ENSE00001181574
chr11:
46701018-46700915
104
RHG01_HUMAN
343-377
35
1
B:366-400
35
1.14d
ENST00000311956
14d
ENSE00001181611
chr11:
46700775-46698630
2146
RHG01_HUMAN
378-439
62
1
B:401-455
55
2.1a
ENST00000400259
1a
ENSE00001132068
chr1:
22379120-22379235
116
CDC42_HUMAN
-
0
0
-
-
2.4
ENST00000400259
4
ENSE00002144782
chr1:
22404922-22405076
155
CDC42_HUMAN
1-35
35
1
A:1-35
35
2.6
ENST00000400259
6
ENSE00000388403
chr1:
22408215-22408287
73
CDC42_HUMAN
36-60
25
1
A:36-60
25
2.7
ENST00000400259
7
ENSE00000759640
chr1:
22412932-22413041
110
CDC42_HUMAN
60-96
37
1
A:60-96
37
2.8b
ENST00000400259
8b
ENSE00000388405
chr1:
22413162-22413359
198
CDC42_HUMAN
97-162
66
1
A:97-162
66
2.10a
ENST00000400259
10a
ENSE00001357650
chr1:
22417921-22419416
1496
CDC42_HUMAN
163-191
29
1
A:163-191
29
[
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]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2ngrb_ (B:)
2a: SCOP_d2ngra_ (A:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
GTPase activation domain, GAP
(18)
Superfamily
:
GTPase activation domain, GAP
(18)
Family
:
BCR-homology GTPase activation domain (BH-domain)
(9)
Protein domain
:
Cdc42GAP
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2ngrb_
B:
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)
2a
d2ngra_
A:
[
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2ngrA00 (A:1-191)
2a: CATH_2ngrB00 (B:260-455)
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)
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)
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)
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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)
Human (Homo sapiens)
(413)
1a
2ngrA00
A:1-191
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Phosphatidylinositol 3-kinase; Chain A
(12)
Homologous Superfamily
:
GTPase -GAP domain
(12)
Human (Homo sapiens)
(10)
2a
2ngrB00
B:260-455
[
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_RhoGAP_2ngrB01 (B:283-431)
2a: PFAM_Ras_2ngrA01 (A:5-178)
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Organisms
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)
Clan
:
GAP
(15)
Family
:
RhoGAP
(12)
Homo sapiens (Human)
(12)
1a
RhoGAP-2ngrB01
B:283-431
Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Homo sapiens (Human)
(141)
2a
Ras-2ngrA01
A:5-178
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