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...
Getting 'PROSITE' information from database.
2RGN
Biol. Unit 1
Info
Asym.Unit (275 KB)
Biol.Unit 1 (136 KB)
Biol.Unit 2 (136 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF P63RHOGEF COMPLEX WITH GALPHA-Q AND RHOA
Authors
:
A. Shankaranarayanan, M. R. Nance, J. J. G. Tesmer
Date
:
04 Oct 07 (Deposition) - 15 Jan 08 (Release) - 07 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Heterotrimeric G-Protein, Small Molecular Weight G-Protein, Signaling Complex, Protein-Protein Complex, Rhogef, Rhoa, Galphaq, Galpha-Q, P63Rhogef, Gq, Gtp-Binding, Lipoprotein, Nucleotide-Binding, Palmitate, Transducer, Adp-Ribosylation, Cytoskeleton, Magnesium, Membrane, Methylation, Prenylation, Proto-Oncogene, Signaling Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Lutz, A. Shankaranarayanan, C. Coco, M. Ridilla, M. R. Nance, C. Vettel, D. Baltus, C. R. Evelyn, R. R. Neubig, T. Wieland, J. J. Tesme
Structure Of Galphaq-P63Rhogef-Rhoa Complex Reveals A Pathway For The Activation Of Rhoa By Gpcrs.
Science V. 318 1923 2007
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: TETRAFLUOROALUMINATE ION (ALFa)
1b: TETRAFLUOROALUMINATE ION (ALFb)
2a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
2b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ALF
1
Ligand/Ion
TETRAFLUOROALUMINATE ION
2
GDP
1
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:48 , GLU A:49 , LYS A:52 , ARG A:183 , PRO A:185 , THR A:186 , GLY A:207 , GLY A:208 , GLN A:209 , GDP A:360 , MG A:362 , HOH A:363 , HOH A:364 , HOH A:365
BINDING SITE FOR RESIDUE ALF A 361
2
AC2
SOFTWARE
SER A:53 , THR A:186 , GDP A:360 , ALF A:361 , HOH A:364 , HOH A:365
BINDING SITE FOR RESIDUE MG A 362
3
AC5
SOFTWARE
GLU A:49 , SER A:50 , GLY A:51 , LYS A:52 , SER A:53 , THR A:54 , SER A:156 , LEU A:180 , ARG A:181 , VAL A:182 , ARG A:183 , ASN A:274 , LYS A:275 , ASP A:277 , CYS A:330 , ALA A:331 , THR A:332 , ALF A:361 , MG A:362 , HOH A:364 , HOH A:365
BINDING SITE FOR RESIDUE GDP A 360
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_039402 (C253Y, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_039402
C
253
Y
ARHGP_HUMAN
Polymorphism
17857333
B
C
253
Y
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: DH_2 (B:160-336)
2: PH_DOMAIN (B:348-466)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DH_2
PS50010
Dbl homology (DH) domain profile.
ARHGP_HUMAN
160-336
1
B:160-336
-
2
PH_DOMAIN
PS50003
PH domain profile.
ARHGP_HUMAN
348-466
1
B:348-466
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2rgna1 (A:67-183)
1b: SCOP_d2rgnd1 (D:67-183)
2a: SCOP_d2rgnc1 (C:4-180)
2b: SCOP_d2rgnf1 (F:5-180)
3a: SCOP_d2rgna2 (A:38-66,A:184-354)
3b: SCOP_d2rgnd2 (D:38-66,D:184-354)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Transducin (alpha subunit), insertion domain
(49)
Superfamily
:
Transducin (alpha subunit), insertion domain
(49)
Family
:
Transducin (alpha subunit), insertion domain
(49)
Protein domain
:
Transducin (alpha subunit), insertion domain
(49)
Mouse (Mus musculus) [TaxId: 10090]
(5)
1a
d2rgna1
A:67-183
1b
d2rgnd1
D:67-183
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)
2a
d2rgnc1
C:4-180
2b
d2rgnf1
F:5-180
Protein domain
:
Transducin (alpha subunit)
(51)
Mouse (Mus musculus) [TaxId: 10090]
(5)
3a
d2rgna2
A:38-66,A:184-354
3b
d2rgnd2
D:38-66,D:184-354
[
close SCOP info
]
CATH Domains
(4, 10)
Info
all CATH domains
1a: CATH_2rgnC00 (C:4-180)
1b: CATH_2rgnF00 (F:5-180)
1c: CATH_2rgnA01 (A:35-67,A:186-358)
1d: CATH_2rgnD01 (D:35-67,D:186-358)
2a: CATH_2rgnA02 (A:68-185)
2b: CATH_2rgnD02 (D:68-185)
3a: CATH_2rgnE01 (E:150-352)
3b: CATH_2rgnB01 (B:149-352)
4a: CATH_2rgnB02 (B:353-490)
4b: CATH_2rgnE02 (E:353-490)
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
2rgnC00
C:4-180
1b
2rgnF00
F:5-180
1c
2rgnA01
A:35-67,A:186-358
1d
2rgnD01
D:35-67,D:186-358
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
GI Alpha 1, domain 2-like
(67)
Homologous Superfamily
:
GI Alpha 1, domain 2-like
(66)
House mouse (Mus musculus)
(4)
2a
2rgnA02
A:68-185
2b
2rgnD02
D:68-185
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)
3a
2rgnE01
E:150-352
3b
2rgnB01
B:149-352
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)
4a
2rgnB02
B:353-490
4b
2rgnE02
E:353-490
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_G_alpha_2rgnD01 (D:37-358)
1b: PFAM_G_alpha_2rgnD02 (D:37-358)
2a: PFAM_Ras_2rgnF01 (F:7-180)
2b: PFAM_Ras_2rgnF02 (F:7-180)
3a: PFAM_RhoGEF_2rgnE01 (E:164-335)
3b: PFAM_RhoGEF_2rgnE02 (E:164-335)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
G-alpha
(24)
Mus musculus (Mouse)
(5)
1a
G-alpha-2rgnD01
D:37-358
1b
G-alpha-2rgnD02
D:37-358
Family
:
Ras
(176)
Homo sapiens (Human)
(141)
2a
Ras-2rgnF01
F:7-180
2b
Ras-2rgnF02
F:7-180
Clan
:
no clan defined [family: RhoGEF]
(22)
Family
:
RhoGEF
(22)
Homo sapiens (Human)
(16)
3a
RhoGEF-2rgnE01
E:164-335
3b
RhoGEF-2rgnE02
E:164-335
[
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
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 (275 KB)
Header - Asym.Unit
Biol.Unit 1 (136 KB)
Header - Biol.Unit 1
Biol.Unit 2 (136 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
2RGN
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help