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3KZ1
Asym. Unit
Info
Asym.Unit (187 KB)
Biol.Unit 1 (93 KB)
Biol.Unit 2 (92 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE COMPLEX OF PDZ-RHOGEF DH/PH DOMAINS WITH GTP-GAMMA-S ACTIVATED RHOA
Authors
:
Z. Chen, P. C. Sternweis, S. R. Sprang
Date
:
07 Dec 09 (Deposition) - 28 Apr 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,E,F
Biol. Unit 1: A,F (1x)
Biol. Unit 2: B,E (1x)
Keywords
:
Regulation Of Rhoa Gtpase, Rhogef, Dh, Ph, Rho, Gtpase Activation, Guanine-Nucleotide Releasing Factor, Membrane, Cytoskeleton, Gtp- Binding, Magnesium, Nucleotide-Binding, Prenylation, Proto-Oncogene, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Chen, F. Medina, M. Y. Liu, C. Thomas, S. R. Sprang, P. C. Sternweis
Activated Rhoa Binds To The Pleckstrin Homology (Ph) Domain Of Pdz-Rhogef, A Potential Site For Autoregulation.
J. Biol. Chem. V. 285 21070 2010
[
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOP... (GSPa)
1b: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOP... (GSPb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GSP
2
Ligand/Ion
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
2
MG
2
Ligand/Ion
MAGNESIUM ION
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR E:19 , THR E:37 , ASP E:59 , GSP E:538
BINDING SITE FOR RESIDUE MG E 550
2
AC2
SOFTWARE
ASP E:13 , ALA E:15 , CYS E:16 , GLY E:17 , LYS E:18 , THR E:19 , CYS E:20 , PHE E:30 , TYR E:34 , THR E:37 , GLY E:62 , LYS E:118 , ASP E:120 , LEU E:121 , ALA E:161 , LYS E:162 , HOH E:207 , MG E:550
BINDING SITE FOR RESIDUE GSP E 538
3
AC3
SOFTWARE
THR F:19 , THR F:37 , ASP F:59 , THR F:60 , GSP F:538
BINDING SITE FOR RESIDUE MG F 550
4
AC4
SOFTWARE
ALA F:15 , CYS F:16 , GLY F:17 , LYS F:18 , THR F:19 , CYS F:20 , PHE F:30 , TYR F:34 , THR F:37 , GLY F:62 , LYS F:118 , ASP F:120 , LEU F:121 , ALA F:161 , LYS F:162 , HOH F:206 , MG F:550
BINDING SITE FOR RESIDUE GSP F 538
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: DH_2 (A:734-923,B:734-923)
2: PH_DOMAIN (A:965-1079,B:965-1079)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DH_2
PS50010
Dbl homology (DH) domain profile.
ARHGB_HUMAN
734-923
2
A:734-923
B:734-923
2
PH_DOMAIN
PS50003
PH domain profile.
ARHGB_HUMAN
965-1079
2
A:965-1079
B:965-1079
[
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Exons
(10, 20)
Info
All Exons
Exon 1.26 (A:714-741 | B:715-741)
Exon 1.27a (A:741-790 | B:741-790)
Exon 1.28 (A:790-816 | B:790-816)
Exon 1.29 (A:817-858 | B:817-858)
Exon 1.30a (A:859-898 | B:859-898)
Exon 1.31b (A:898-957 | B:898-957)
Exon 1.32 (A:958-983 | B:958-983)
Exon 1.33 (A:983-1039 (gaps) | B:983-1039 (ga...)
Exon 1.34 (A:1039-1069 | B:1039-1069)
Exon 1.35 (A:1069-1082 | B:1069-1081)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.25/1.26
02: Boundary 1.26/1.27a
03: Boundary 1.27a/1.28
04: Boundary 1.28/1.29
05: Boundary 1.29/1.30a
06: Boundary 1.30a/1.31b
07: Boundary 1.31b/1.32
08: Boundary 1.32/1.33
09: Boundary 1.33/1.34
10: Boundary 1.34/1.35
11: Boundary 1.35/1.36
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
1.1b
ENST00000361409
1b
ENSE00001839709
chr1:
157014865-157014091
775
ARHGB_HUMAN
1-11
11
0
-
-
1.2
ENST00000361409
2
ENSE00001436720
chr1:
156955965-156955874
92
ARHGB_HUMAN
11-42
32
0
-
-
1.3
ENST00000361409
3
ENSE00000904836
chr1:
156954229-156954131
99
ARHGB_HUMAN
42-75
34
0
-
-
1.4
ENST00000361409
4
ENSE00000904837
chr1:
156950278-156950229
50
ARHGB_HUMAN
75-91
17
0
-
-
1.5
ENST00000361409
5
ENSE00000904838
chr1:
156949078-156949021
58
ARHGB_HUMAN
92-111
20
0
-
-
1.6
ENST00000361409
6
ENSE00000904839
chr1:
156948174-156947996
179
ARHGB_HUMAN
111-170
60
0
-
-
1.7
ENST00000361409
7
ENSE00000904840
chr1:
156946846-156946775
72
ARHGB_HUMAN
171-194
24
0
-
-
1.9
ENST00000361409
9
ENSE00000904841
chr1:
156939835-156939790
46
ARHGB_HUMAN
195-210
16
0
-
-
1.10
ENST00000361409
10
ENSE00000904842
chr1:
156939150-156939074
77
ARHGB_HUMAN
210-235
26
0
-
-
1.11a
ENST00000361409
11a
ENSE00000904843
chr1:
156937916-156937779
138
ARHGB_HUMAN
236-281
46
0
-
-
1.13
ENST00000361409
13
ENSE00000904844
chr1:
156933386-156933312
75
ARHGB_HUMAN
282-306
25
0
-
-
1.14
ENST00000361409
14
ENSE00000904845
chr1:
156933096-156932995
102
ARHGB_HUMAN
307-340
34
0
-
-
1.15
ENST00000361409
15
ENSE00001195452
chr1:
156931567-156931469
99
ARHGB_HUMAN
341-373
33
0
-
-
1.16
ENST00000361409
16
ENSE00000904847
chr1:
156930252-156930210
43
ARHGB_HUMAN
374-388
15
0
-
-
1.17
ENST00000361409
17
ENSE00000904848
chr1:
156928934-156928838
97
ARHGB_HUMAN
388-420
33
0
-
-
1.18
ENST00000361409
18
ENSE00000904849
chr1:
156928656-156928534
123
ARHGB_HUMAN
420-461
42
0
-
-
1.19
ENST00000361409
19
ENSE00001436165
chr1:
156927607-156927584
24
ARHGB_HUMAN
461-469
9
0
-
-
1.20
ENST00000361409
20
ENSE00001436260
chr1:
156926356-156926212
145
ARHGB_HUMAN
469-517
49
0
-
-
1.21b
ENST00000361409
21b
ENSE00001074420
chr1:
156925591-156925495
97
ARHGB_HUMAN
518-550
33
0
-
-
1.22
ENST00000361409
22
ENSE00001195422
chr1:
156924713-156924684
30
ARHGB_HUMAN
550-560
11
0
-
-
1.23
ENST00000361409
23
ENSE00001054866
chr1:
156921491-156921365
127
ARHGB_HUMAN
560-602
43
0
-
-
1.24
ENST00000361409
24
ENSE00000904853
chr1:
156918290-156918111
180
ARHGB_HUMAN
602-662
61
0
-
-
1.25
ENST00000361409
25
ENSE00001195407
chr1:
156918020-156917973
48
ARHGB_HUMAN
662-678
17
0
-
-
1.26
ENST00000361409
26
ENSE00000904855
chr1:
156917748-156917561
188
ARHGB_HUMAN
678-741
64
2
A:714-741
B:715-741
28
27
1.27a
ENST00000361409
27a
ENSE00000904856
chr1:
156917242-156917096
147
ARHGB_HUMAN
741-790
50
2
A:741-790
B:741-790
50
50
1.28
ENST00000361409
28
ENSE00000904857
chr1:
156916807-156916728
80
ARHGB_HUMAN
790-816
27
2
A:790-816
B:790-816
27
27
1.29
ENST00000361409
29
ENSE00000904858
chr1:
156916579-156916454
126
ARHGB_HUMAN
817-858
42
2
A:817-858
B:817-858
42
42
1.30a
ENST00000361409
30a
ENSE00000904859
chr1:
156915954-156915837
118
ARHGB_HUMAN
859-898
40
2
A:859-898
B:859-898
40
40
1.31b
ENST00000361409
31b
ENSE00001253778
chr1:
156914989-156914811
179
ARHGB_HUMAN
898-957
60
2
A:898-957
B:898-957
60
60
1.32
ENST00000361409
32
ENSE00001195373
chr1:
156914225-156914150
76
ARHGB_HUMAN
958-983
26
2
A:958-983
B:958-983
26
26
1.33
ENST00000361409
33
ENSE00000904862
chr1:
156913894-156913727
168
ARHGB_HUMAN
983-1039
57
2
A:983-1039 (gaps)
B:983-1039 (gaps)
57
57
1.34
ENST00000361409
34
ENSE00000904863
chr1:
156912572-156912482
91
ARHGB_HUMAN
1039-1069
31
2
A:1039-1069
B:1039-1069
31
31
1.35
ENST00000361409
35
ENSE00000904864
chr1:
156911781-156911656
126
ARHGB_HUMAN
1069-1111
43
2
A:1069-1082
B:1069-1081
14
13
1.36
ENST00000361409
36
ENSE00000904865
chr1:
156911225-156911164
62
ARHGB_HUMAN
1111-1132
22
0
-
-
1.37a
ENST00000361409
37a
ENSE00000904866
chr1:
156910217-156909999
219
ARHGB_HUMAN
1132-1205
74
0
-
-
1.37c
ENST00000361409
37c
ENSE00001253771
chr1:
156909702-156909340
363
ARHGB_HUMAN
1205-1326
122
0
-
-
1.37f
ENST00000361409
37f
ENSE00001195338
chr1:
156908305-156908210
96
ARHGB_HUMAN
1326-1358
33
0
-
-
1.38
ENST00000361409
38
ENSE00001253710
chr1:
156907288-156907041
248
ARHGB_HUMAN
1358-1440
83
0
-
-
1.39
ENST00000361409
39
ENSE00000904870
chr1:
156906797-156906608
190
ARHGB_HUMAN
1441-1504
64
0
-
-
1.40a
ENST00000361409
40a
ENSE00001847612
chr1:
156905850-156905316
535
ARHGB_HUMAN
1504-1522
19
0
-
-
[
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SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d3kz1a1 (A:714-941)
1b: SCOP_d3kz1b1 (B:715-941)
2a: SCOP_d3kz1a2 (A:942-1082)
2b: SCOP_d3kz1b2 (B:942-1081)
3a: SCOP_d3kz1e_ (E:)
3b: SCOP_d3kz1f_ (F:)
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Protein Domains
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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 11, PDZ-RhoGEF
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d3kz1a1
A:714-941
1b
d3kz1b1
B:715-941
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 11, PDZ-RhoGEF
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
2a
d3kz1a2
A:942-1082
2b
d3kz1b2
B:942-1081
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
:
RhoA
(19)
Human (Homo sapiens) [TaxId: 9606]
(19)
3a
d3kz1e_
E:
3b
d3kz1f_
F:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3kz1E00 (E:3-181)
1b: CATH_3kz1F00 (F:3-181)
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Homologous Superfamilies
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(
)
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
3kz1E00
E:3-181
1b
3kz1F00
F:3-181
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Ras_3kz1F01 (F:7-180)
1b: PFAM_Ras_3kz1F02 (F:7-180)
2a: PFAM_RhoGEF_3kz1B01 (B:738-922)
2b: PFAM_RhoGEF_3kz1B02 (B:738-922)
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Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Homo sapiens (Human)
(141)
1a
Ras-3kz1F01
F:7-180
1b
Ras-3kz1F02
F:7-180
Clan
:
no clan defined [family: RhoGEF]
(22)
Family
:
RhoGEF
(22)
Homo sapiens (Human)
(16)
2a
RhoGEF-3kz1B01
B:738-922
2b
RhoGEF-3kz1B02
B:738-922
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