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.
3NS8
Asym. Unit
Info
Asym.Unit (33 KB)
Biol.Unit 1 (29 KB)
Biol.Unit 2 (16 KB)
Biol.Unit 3 (15 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 AN OPEN CONFORMATION OF LYS48-LINKED DIUBIQUITIN AT PH 7.5
Authors
:
D. Zhang, N. Laronde-Leblanc, D. Fushman
Date
:
01 Jul 10 (Deposition) - 20 Jul 11 (Release) - 17 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.71
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A (1x)
Biol. Unit 3: B (1x)
Keywords
:
Diubiquitin, Isopeptide Bond, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Y. Lai, D. Zhang, N. Laronde-Leblanc, D. Fushman
Structural And Biochemical Studies Of The Open State Of Lys48-Linked Diubiquitin.
Biochim. Biophys. Acta V. 1823 2046 2012
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2
GOL
2
Ligand/Ion
GLYCEROL
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:51 , ASP A:52 , ARG A:72 , HOH A:81 , HOH A:102 , HOH A:111 , GLY B:47 , LYS B:48 , GLN B:49
BINDING SITE FOR RESIDUE GOL A 77
2
AC2
SOFTWARE
LYS A:48 , GLN A:49 , HOH A:90 , HOH A:130 , LYS B:27 , GLN B:49 , LEU B:50 , GLU B:51 , ASP B:52 , ARG B:72 , HOH B:96
BINDING SITE FOR RESIDUE GOL B 77
3
AC3
SOFTWARE
ASN B:25 , ALA B:28 , LYS B:29 , ASP B:32 , PHE B:45 , SER B:65 , THR B:66 , HIS B:68 , HOH B:87 , HOH B:95 , HOH B:124
BINDING SITE FOR RESIDUE EPE B 78
[
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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (A:1-76,B:1-73,A:1-76,B:1-73,-|-|A:...)
2: UBIQUITIN_1 (A:27-52,B:27-52,A:27-52,B: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_HUMAN
1-76
2
A:1-76
B:1-73
RL40_HUMAN
1-76
2
A:1-76
B:1-73
UBB_HUMAN
1-76
77-152
153-228
2
-
-
A:1-76
B:1-73
UBC_HUMAN
1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
2
-
-
-
-
-
-
-
-
A:1-76
B:1-73
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
RS27A_HUMAN
27-52
2
A:27-52
B:27-52
RL40_HUMAN
27-52
2
A:27-52
B:27-52
UBB_HUMAN
27-52
103-128
179-204
2
-
-
A:27-52
B:27-52
UBC_HUMAN
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
[
close PROSITE info
]
Exons
(1, 2)
Info
All Exons
Exon 1.2 (A:1-76 | B:1-73)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/-
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
1.1
ENST00000339647
1
ENSE00001257182
chr12:
125399577-125399133
445
UBC_HUMAN
-
0
0
-
-
1.2
ENST00000339647
2
ENSE00001406973
chr12:
125398320-125396194
2127
UBC_HUMAN
1-686
686
2
A:1-76
B:1-73
76
73
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3ns8a_ (A:)
1b: SCOP_d3ns8b_ (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)
Human (Homo sapiens) [TaxId: 9606]
(121)
1a
d3ns8a_
A:
1b
d3ns8b_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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
Biol.Unit 2 (16 KB)
Header - Biol.Unit 2
Biol.Unit 3 (15 KB)
Header - Biol.Unit 3
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
3NS8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
