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.
PLEASE WAIT...
Getting 'Exon' information from database.
3ZJD
Asym. Unit
Info
Asym.Unit (233 KB)
Biol.Unit 1 (226 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
A20 OTU DOMAIN IN REDUCED, ACTIVE STATE AT 1.87 A RESOLUTION
Authors
:
Y. Kulathu, F. J. Garcia, T. E. T. Mevissen, M. Busch, N. Arnaudo, K. S. Ca D. Barford, D. Komander
Date
:
17 Jan 13 (Deposition) - 06 Mar 13 (Release) - 20 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.87
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hydrolase, Ubiquitin, Deubiquitinating Enzyme, Reversible Oxidation, Sulphenic Acid, Cys Protease
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Kulathu, F. J. Garcia, T. E. T. Mevissen, M. Busch, N. Arnaudo, K. S. Carroll, D. Barford, D. Komander
Regulation Of A20 And Other Otu Deubiquitinases By Reversible Oxidation
Nat. Commun. V. 4 1569 2013
[
close entry info
]
Hetero Components
(2, 6)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
2a: 1,2-ETHANEDIOL (EDOa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
5
Ligand/Ion
CHLORIDE ION
2
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS B:86 , ARG B:87 , ARG B:278 , HOH B:2039
BINDING SITE FOR RESIDUE CL B1358
2
AC2
SOFTWARE
GLU A:311 , GLY B:281 , TRP B:317
BINDING SITE FOR RESIDUE CL B1359
3
AC3
SOFTWARE
MET A:308 , TRP B:317 , ASP B:318 , HIS B:323
BINDING SITE FOR RESIDUE CL B1360
4
AC4
SOFTWARE
GLY A:230 , GLY A:231 , LYS A:287 , HOH A:2098
BINDING SITE FOR RESIDUE CL A1357
5
AC5
SOFTWARE
ARG B:45 , CYS B:243 , TYR B:244 , HOH B:2016
BINDING SITE FOR RESIDUE CL B1361
6
AC6
SOFTWARE
LEU A:275 , ASP A:285 , LEU A:286 , LYS A:299 , GLU A:300 , LEU A:303 , ASN A:326 , HOH A:2119
BINDING SITE FOR RESIDUE EDO A1358
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020447 (A125V, chain A/B, )
2: VAR_022143 (F127C, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020447
A
125
V
TNAP3_HUMAN
Polymorphism
5029941
A/B
A
125
V
2
UniProt
VAR_022143
F
127
C
TNAP3_HUMAN
Polymorphism
2230926
A/B
F
127
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: OTU (A:92-263,B:92-263)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
OTU
PS50802
OTU domain profile.
TNAP3_HUMAN
92-263
2
A:92-263
B:92-263
[
close PROSITE info
]
Exons
(6, 12)
Info
All Exons
Exon 1.3b (A:5-99 | B:6-99)
Exon 1.4 (A:99-149 | B:99-149)
Exon 1.5 (A:163-212 (gaps) | B:164-212 (gaps...)
Exon 1.6b (A:212-269 (gaps) | B:212-269 (gaps...)
Exon 1.7 (A:269-329 | B:269-329)
Exon 1.8b (A:329-356 | B:329-357)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1c/1.3b
2: Boundary 1.3b/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6b
5: Boundary 1.6b/1.7
6: Boundary 1.7/1.8b
7: Boundary 1.8b/1.9
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
1.1c
ENST00000237289
1c
ENSE00001013057
chr6:
138188581-138188631
51
TNAP3_HUMAN
-
0
0
-
-
1.3b
ENST00000237289
3b
ENSE00002202018
chr6:
138192350-138192659
310
TNAP3_HUMAN
1-99
99
2
A:5-99
B:6-99
95
94
1.4
ENST00000237289
4
ENSE00002197706
chr6:
138195982-138196172
191
TNAP3_HUMAN
99-162
64
2
A:99-149
B:99-149
51
51
1.5
ENST00000237289
5
ENSE00000764532
chr6:
138196825-138196972
148
TNAP3_HUMAN
163-212
50
2
A:163-212 (gaps)
B:164-212 (gaps)
50
49
1.6b
ENST00000237289
6b
ENSE00000764533
chr6:
138197133-138197303
171
TNAP3_HUMAN
212-269
58
2
A:212-269 (gaps)
B:212-269 (gaps)
58
58
1.7
ENST00000237289
7
ENSE00002165528
chr6:
138198213-138198393
181
TNAP3_HUMAN
269-329
61
2
A:269-329
B:269-329
61
61
1.8b
ENST00000237289
8b
ENSE00000764536
chr6:
138199569-138200488
920
TNAP3_HUMAN
329-636
308
2
A:329-356
B:329-357
28
29
1.9
ENST00000237289
9
ENSE00000764537
chr6:
138201208-138201389
182
TNAP3_HUMAN
636-696
61
0
-
-
1.10
ENST00000237289
10
ENSE00000798910
chr6:
138202172-138204449
2278
TNAP3_HUMAN
697-790
94
0
-
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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 (233 KB)
Header - Asym.Unit
Biol.Unit 1 (226 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
3ZJD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
