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.
2D3G
Asym. Unit
Info
Asym.Unit (33 KB)
Biol.Unit 1 (29 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
DOUBLE SIDED UBIQUITIN BINDING OF HRS-UIM
Authors
:
S. Hirano, M. Kawasaki, R. Kato, S. Wakatsuki
Date
:
28 Sep 05 (Deposition) - 20 Dec 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,P
Biol. Unit 1: A,B,P (1x)
Keywords
:
Protein-Protein Complex, Uim And Ubiquitin, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Hirano, M. Kawasaki, H. Ura, R. Kato, C. Raiborg, H. Stenmark, S. Wakatsuki
Double-Sided Ubiquitin Binding Of Hrs-Uim In Endosomal Protein Sorting
Nat. Struct. Mol. Biol. V. 13 272 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
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 not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 5)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (A:1-72,B:1-72,A:1-72,B:1-72,-|-|-|...)
2: UBIQUITIN_1 (A:27-52,B:27-52,A:27-52,B:27-52,-|...)
3: UIM (P:258-274)
;
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
2
A:1-72
B:1-72
RL40_BOVIN
1-76
2
A:1-72
B:1-72
UBB_BOVIN
1-76
77-152
153-228
229-304
2
-
-
-
A:1-72
B:1-72
UBC_BOVIN
1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
2
-
-
-
-
-
-
-
-
A:1-72
B:1-72
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
RS27A_BOVIN
27-52
2
A:27-52
B:27-52
RL40_BOVIN
27-52
2
A:27-52
B:27-52
UBB_BOVIN
27-52
103-128
179-204
255-280
2
-
-
-
A:27-52
B:27-52
UBC_BOVIN
27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
2
-
-
-
-
-
-
-
-
A:27-52
B:27-52
3
UIM
PS50330
Ubiquitin-interacting motif (UIM) domain profile.
HGS_HUMAN
258-277
1
P:258-274
[
close PROSITE info
]
Exons
(1, 1)
Info
All Exons
Exon 1.10 (P:257-274)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.9/1.10
2: Boundary 1.10/1.11
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
1.1a
ENST00000329138
1a
ENSE00001391303
chr17:
79651020-79651133
114
HGS_HUMAN
1-13
13
0
-
-
1.2
ENST00000329138
2
ENSE00001308807
chr17:
79652635-79652719
85
HGS_HUMAN
13-41
29
0
-
-
1.3
ENST00000329138
3
ENSE00001325636
chr17:
79653342-79653417
76
HGS_HUMAN
41-66
26
0
-
-
1.4
ENST00000329138
4
ENSE00001314149
chr17:
79654033-79654125
93
HGS_HUMAN
67-97
31
0
-
-
1.5
ENST00000329138
5
ENSE00001296740
chr17:
79655734-79655857
124
HGS_HUMAN
98-139
42
0
-
-
1.6
ENST00000329138
6
ENSE00001316542
chr17:
79657212-79657264
53
HGS_HUMAN
139-156
18
0
-
-
1.7
ENST00000329138
7
ENSE00001292653
chr17:
79657704-79657772
69
HGS_HUMAN
157-179
23
0
-
-
1.8
ENST00000329138
8
ENSE00001306492
chr17:
79658477-79658601
125
HGS_HUMAN
180-221
42
0
-
-
1.9
ENST00000329138
9
ENSE00001296588
chr17:
79660533-79660611
79
HGS_HUMAN
221-247
27
0
-
-
1.10
ENST00000329138
10
ENSE00001313160
chr17:
79660684-79660782
99
HGS_HUMAN
248-280
33
1
P:257-274
18
1.11
ENST00000329138
11
ENSE00001292556
chr17:
79660900-79660995
96
HGS_HUMAN
281-312
32
0
-
-
1.12
ENST00000329138
12
ENSE00001314367
chr17:
79661845-79661883
39
HGS_HUMAN
313-325
13
0
-
-
1.13
ENST00000329138
13
ENSE00001303643
chr17:
79661954-79662097
144
HGS_HUMAN
326-373
48
0
-
-
1.14
ENST00000329138
14
ENSE00001321161
chr17:
79662194-79662253
60
HGS_HUMAN
374-393
20
0
-
-
1.15
ENST00000329138
15
ENSE00001299855
chr17:
79662816-79663029
214
HGS_HUMAN
394-465
72
0
-
-
1.16b
ENST00000329138
16b
ENSE00001299623
chr17:
79663387-79663559
173
HGS_HUMAN
465-522
58
0
-
-
1.17
ENST00000329138
17
ENSE00001301435
chr17:
79663637-79663777
141
HGS_HUMAN
523-569
47
0
-
-
1.18a
ENST00000329138
18a
ENSE00001421749
chr17:
79663854-79664028
175
HGS_HUMAN
570-628
59
0
-
-
1.19
ENST00000329138
19
ENSE00001300174
chr17:
79667497-79667630
134
HGS_HUMAN
628-672
45
0
-
-
1.20
ENST00000329138
20
ENSE00001320441
chr17:
79667725-79667844
120
HGS_HUMAN
673-712
40
0
-
-
1.21
ENST00000329138
21
ENSE00001296545
chr17:
79668075-79668161
87
HGS_HUMAN
713-741
29
0
-
-
1.22a
ENST00000329138
22a
ENSE00001319441
chr17:
79668538-79669143
606
HGS_HUMAN
742-777
36
0
-
-
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2d3ga_ (A:)
1b: SCOP_d2d3gb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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)
1a
d2d3ga_
A:
1b
d2d3gb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2d3gA00 (A:1-72)
1b: CATH_2d3gB00 (B:1-72)
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)
Cattle (Bos taurus)
(10)
1a
2d3gA00
A:1-72
1b
2d3gB00
B:1-72
[
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 A
Chain B
Chain P
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 (33 KB)
Header - Asym.Unit
Biol.Unit 1 (29 KB)
Header - Biol.Unit 1
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
2D3G
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
