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.
1WR6
Biol. Unit 2
Info
Asym.Unit (113 KB)
Biol.Unit 1 (29 KB)
Biol.Unit 2 (29 KB)
Biol.Unit 3 (29 KB)
Biol.Unit 4 (29 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 GGA3 GAT DOMAIN IN COMPLEX WITH UBIQUITIN
Authors
:
M. Kawasaki, T. Shiba, Y. Shiba, Y. Yamaguchi, N. Matsugaki, N. Igarashi, M. Suzuki, R. Kato, K. Kato, K. Nakayama, S. Wakatsuki
Date
:
12 Oct 04 (Deposition) - 28 Jun 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E (1x)
Biol. Unit 2: B,F (1x)
Biol. Unit 3: C,G (1x)
Biol. Unit 4: D,H (1x)
Keywords
:
Three-Helix Bundle, Ubiquitin-Binding Protein, Clathrin Coat Adaptor Protein, Protein Transport/Signaling Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Kawasaki, T. Shiba, Y. Shiba, Y. Yamaguchi, N. Matsugaki, N. Igarashi, M. Suzuki, R. Kato, K. Kato, K. Nakayama, S. Wakatsuki
Molecular Mechanism Of Ubiquitin Recognition By Gga3 Gat Domain.
Genes Cells V. 10 639 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
2
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (F:1-73)
2: UBIQUITIN_1 (F:27-52)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UBIQUITIN_2
PS50053
Ubiquitin domain profile.
RS27A_BOVIN
1-76
1
-
F:1-73
-
-
RL40_BOVIN
1-76
1
-
F:1-73
-
-
UBB_BOVIN
1-76
77-152
153-228
229-304
1
-
-
-
-
F:1-73
-
-
UBC_BOVIN
1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
1
-
-
-
-
-
-
-
-
-
F:1-73
-
-
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
RS27A_BOVIN
27-52
1
-
F:27-52
-
-
RL40_BOVIN
27-52
1
-
F:27-52
-
-
UBB_BOVIN
27-52
103-128
179-204
255-280
1
-
-
-
-
F:27-52
-
-
UBC_BOVIN
27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
1
-
-
-
-
-
-
-
-
-
F:27-52
-
-
[
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1wr6a1 (A:211-300)
1b: SCOP_d1wr6b_ (B:)
1c: SCOP_d1wr6c_ (C:)
1d: SCOP_d1wr6d_ (D:)
2a: SCOP_d1wr6e_ (E:)
2b: SCOP_d1wr6f_ (F:)
2c: SCOP_d1wr6g_ (G:)
2d: SCOP_d1wr6h_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Spectrin repeat-like
(186)
Superfamily
:
GAT-like domain
(16)
Family
:
GAT domain
(9)
Protein domain
:
ADP-ribosylation factor binding protein Gga3
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1wr6a1
A:211-300
1b
d1wr6b_
B:
1c
d1wr6c_
C:
1d
d1wr6d_
D:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
Ubiquitin-like
(546)
Family
:
Ubiquitin-related
(337)
Protein domain
:
Ubiquitin
(162)
Cow (Bos taurus) [TaxId: 9913]
(24)
2a
d1wr6e_
E:
2b
d1wr6f_
F:
2c
d1wr6g_
G:
2d
d1wr6h_
H:
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1wr6H00 (H:1-74)
1b: CATH_1wr6F00 (F:1-73)
1c: CATH_1wr6E00 (E:1-72)
1d: CATH_1wr6G00 (G:1-72)
2a: CATH_1wr6A00 (A:211-300)
2b: CATH_1wr6B00 (B:215-304)
2c: CATH_1wr6C00 (C:212-301)
2d: CATH_1wr6D00 (D:215-302)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
(286)
Human (Homo sapiens)
(177)
1a
1wr6H00
H:1-74
1b
1wr6F00
F:1-73
1c
1wr6E00
E:1-72
1d
1wr6G00
G:1-72
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Methane Monooxygenase Hydroxylase; Chain G, domain 1
(192)
Homologous Superfamily
:
[code=1.20.58.160, no name defined]
(7)
Human (Homo sapiens)
(6)
2a
1wr6A00
A:211-300
2b
1wr6B00
B:215-304
2c
1wr6C00
C:212-301
2d
1wr6D00
D:215-302
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 B
Chain F
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 (113 KB)
Header - Asym.Unit
Biol.Unit 1 (29 KB)
Header - Biol.Unit 1
Biol.Unit 2 (29 KB)
Header - Biol.Unit 2
Biol.Unit 3 (29 KB)
Header - Biol.Unit 3
Biol.Unit 4 (29 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
1WR6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help