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.
1Y3A
Asym. Unit
Info
Asym.Unit (217 KB)
Biol.Unit 1 (205 KB)
Biol.Unit 2 (6 KB)
Biol.Unit 3 (6 KB)
Biol.Unit 4 (6 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF G-ALPHA-I1 BOUND TO A GDP-SELECTIVE PEPTIDE PROVIDES INSIGHT INTO GUANINE NUCLEOTIDE EXCHANGE
Authors
:
C. A. Johnston, F. S. Willard, M. R. Jezyk, Z. Fredericks, E. T. Bodor, M. B. Jones, R. Blaesius, T. K. Harden, J. Sondek, V. J. Watts, J. K. Ramer, D. P. Siderovski
Date
:
24 Nov 04 (Deposition) - 12 Jul 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: F (1x)
Biol. Unit 3: G (1x)
Biol. Unit 4: H (1x)
Keywords
:
Protein-Peptide Complex, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. A. Johnston, F. S. Willard, M. R. Jezyk, Z. Fredericks, E. T. Bodor, M. B. Jones, R. Blaesius, V. J. Watts, T. K. Harden, J. Sondek, J. K. Ramer, D. P. Siderovski
Structure Of G-Alpha-I1 Bound To A Gdp-Selective Peptide Provides Insight Into Guanine Nucleotide Exchange
Structure V. 7 1069 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
1b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
1c: GUANOSINE-5'-DIPHOSPHATE (GDPc)
1d: GUANOSINE-5'-DIPHOSPHATE (GDPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GDP
4
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
[
close Hetero Component info
]
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
GLY A:42 , GLU A:43 , SER A:44 , GLY A:45 , LYS A:46 , SER A:47 , THR A:48 , ASP A:150 , LEU A:175 , ARG A:176 , ARG A:178 , ASN A:269 , LYS A:270 , ASP A:272 , LEU A:273 , CYS A:325 , ALA A:326 , THR A:327 , HOH A:358 , HOH A:372
BINDING SITE FOR RESIDUE GDP A 355
2
AC2
SOFTWARE
GLU B:43 , SER B:44 , GLY B:45 , LYS B:46 , SER B:47 , THR B:48 , ASP B:150 , LEU B:175 , ARG B:176 , THR B:177 , ARG B:178 , ASN B:269 , LYS B:270 , ASP B:272 , LEU B:273 , CYS B:325 , ALA B:326 , THR B:327 , HOH B:358 , HOH B:365 , HOH B:366
BINDING SITE FOR RESIDUE GDP B 356
3
AC3
SOFTWARE
GLY C:42 , GLU C:43 , SER C:44 , GLY C:45 , LYS C:46 , SER C:47 , THR C:48 , ASP C:150 , LEU C:175 , ARG C:176 , THR C:177 , ARG C:178 , ASN C:269 , LYS C:270 , ASP C:272 , LEU C:273 , CYS C:325 , ALA C:326 , THR C:327 , HOH C:362 , HOH C:367
BINDING SITE FOR RESIDUE GDP C 357
4
AC4
SOFTWARE
GLY D:42 , GLU D:43 , SER D:44 , GLY D:45 , LYS D:46 , SER D:47 , THR D:48 , ASP D:150 , LEU D:175 , ARG D:176 , THR D:177 , ARG D:178 , ASN D:269 , LYS D:270 , ASP D:272 , LEU D:273 , CYS D:325 , ALA D:326 , THR D:327 , HOH D:372 , HOH D:374
BINDING SITE FOR RESIDUE GDP D 358
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(8, 32)
Info
All Exons
Exon 1.4a (A:34-40 | B:34-40 | C:34-40 | D:34...)
Exon 1.8 (A:40-54 | B:40-54 | C:40-54 | D:40...)
Exon 1.9b (A:54-101 | B:54-101 | C:54-101 | D...)
Exon 1.10 (A:102-154 (gaps) | B:102-154 (gaps...)
Exon 1.11 (A:154-197 | B:154-197 | C:154-197 ...)
Exon 1.12 (A:197-240 (gaps) | B:197-240 | C:1...)
Exon 1.13 (A:241-292 | B:241-292 | C:241-292 ...)
Exon 1.14b (A:292-345 | B:292-344 | C:292-344 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.4a
2: Boundary 1.4a/1.8
3: Boundary 1.8/1.9b
4: Boundary 1.9b/1.10
5: Boundary 1.10/1.11
6: Boundary 1.11/1.12
7: Boundary 1.12/1.13
8: Boundary 1.13/1.14b
9: Boundary 1.14b/-
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
1.4a
ENST00000351004
4a
ENSE00001371927
chr7:
79764104-79764594
491
GNAI1_HUMAN
1-40
40
4
A:34-40
B:34-40
C:34-40
D:34-40
7
7
7
7
1.8
ENST00000351004
8
ENSE00001626524
chr7:
79818267-79818309
43
GNAI1_HUMAN
40-54
15
4
A:40-54
B:40-54
C:40-54
D:40-54
15
15
15
15
1.9b
ENST00000351004
9b
ENSE00001129655
chr7:
79818406-79818547
142
GNAI1_HUMAN
54-101
48
4
A:54-101
B:54-101
C:54-101
D:54-101
48
48
48
48
1.10
ENST00000351004
10
ENSE00000877050
chr7:
79828541-79828698
158
GNAI1_HUMAN
102-154
53
4
A:102-154 (gaps)
B:102-154 (gaps)
C:102-154 (gaps)
D:102-154 (gaps)
53
53
53
53
1.11
ENST00000351004
11
ENSE00002174891
chr7:
79833020-79833148
129
GNAI1_HUMAN
154-197
44
4
A:154-197
B:154-197
C:154-197
D:154-197
44
44
44
44
1.12
ENST00000351004
12
ENSE00001369917
chr7:
79840285-79840414
130
GNAI1_HUMAN
197-240
44
4
A:197-240 (gaps)
B:197-240
C:197-240 (gaps)
D:197-240
44
44
44
44
1.13
ENST00000351004
13
ENSE00001591517
chr7:
79842032-79842185
154
GNAI1_HUMAN
241-292
52
4
A:241-292
B:241-292
C:241-292
D:241-292
52
52
52
52
1.14b
ENST00000351004
14b
ENSE00001303419
chr7:
79846619-79848718
2100
GNAI1_HUMAN
292-354
63
4
A:292-345
B:292-344
C:292-344
D:292-344
54
53
53
53
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1y3aa1 (A:61-181)
1b: SCOP_d1y3ab1 (B:61-181)
1c: SCOP_d1y3ac1 (C:61-181)
1d: SCOP_d1y3ad1 (D:61-181)
2a: SCOP_d1y3aa2 (A:34-60,A:182-345)
2b: SCOP_d1y3ab2 (B:34-60,B:182-344)
2c: SCOP_d1y3ac2 (C:34-60,C:182-344)
2d: SCOP_d1y3ad2 (D:34-60,D:182-344)
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)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d1y3aa1
A:61-181
1b
d1y3ab1
B:61-181
1c
d1y3ac1
C:61-181
1d
d1y3ad1
D:61-181
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
:
Transducin (alpha subunit)
(51)
Human (Homo sapiens) [TaxId: 9606]
(7)
2a
d1y3aa2
A:34-60,A:182-345
2b
d1y3ab2
B:34-60,B:182-344
2c
d1y3ac2
C:34-60,C:182-344
2d
d1y3ad2
D:34-60,D:182-344
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1y3aB01 (B:34-61,B:181-343)
1b: CATH_1y3aD01 (D:34-61,D:181-343)
1c: CATH_1y3aA01 (A:34-61,A:181-343)
1d: CATH_1y3aC01 (C:34-61,C:181-343)
2a: CATH_1y3aB02 (B:62-180)
2b: CATH_1y3aD02 (D:62-180)
2c: CATH_1y3aA02 (A:62-180)
2d: CATH_1y3aC02 (C:62-180)
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)
Human (Homo sapiens)
(413)
1a
1y3aB01
B:34-61,B:181-343
1b
1y3aD01
D:34-61,D:181-343
1c
1y3aA01
A:34-61,A:181-343
1d
1y3aC01
C:34-61,C:181-343
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)
Human (Homo sapiens)
(13)
2a
1y3aB02
B:62-180
2b
1y3aD02
D:62-180
2c
1y3aA02
A:62-180
2d
1y3aC02
C:62-180
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_G_alpha_1y3aD01 (D:34-344)
1b: PFAM_G_alpha_1y3aD02 (D:34-344)
1c: PFAM_G_alpha_1y3aD03 (D:34-344)
1d: PFAM_G_alpha_1y3aD04 (D:34-344)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
G-alpha
(24)
Homo sapiens (Human)
(6)
1a
G-alpha-1y3aD01
D:34-344
1b
G-alpha-1y3aD02
D:34-344
1c
G-alpha-1y3aD03
D:34-344
1d
G-alpha-1y3aD04
D:34-344
[
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
Chain E
Chain F
Chain G
Chain H
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 (217 KB)
Header - Asym.Unit
Biol.Unit 1 (205 KB)
Header - Biol.Unit 1
Biol.Unit 2 (6 KB)
Header - Biol.Unit 2
Biol.Unit 3 (6 KB)
Header - Biol.Unit 3
Biol.Unit 4 (6 KB)
Header - Biol.Unit 4
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
1Y3A
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help