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.
3TRT
Asym. Unit
Info
Asym.Unit (58 KB)
Biol.Unit 1 (52 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 STABILISED VIMENTIN COIL2 FRAGMENT
Authors
:
A. A. Chernyatina, S. V. Strelkov
Date
:
10 Sep 11 (Deposition) - 01 Feb 12 (Release) - 01 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Cytoskeleton, Intermediate Filament, Vimentin, Alpha-Helix, Structural Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. A. Chernyatina, S. V. Strelkov
Stabilization Of Vimentin Coil2 Fragment Via An Engineered Disulfide.
J. Struct. Biol. V. 177 46 2012
[
close entry info
]
Hetero Components
(4, 12)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
3a: AMMONIUM ION (NH4a)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
3
Ligand/Ion
GLYCEROL
2
MSE
4
Mod. Amino Acid
SELENOMETHIONINE
3
NH4
1
Ligand/Ion
AMMONIUM ION
4
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:310 , GLN A:314
BINDING SITE FOR RESIDUE SO4 A 2
2
AC2
SOFTWARE
NH4 A:8 , GLN A:274
BINDING SITE FOR RESIDUE SO4 A 4
3
AC3
SOFTWARE
ALA A:280 , ASN A:283 , HOH B:33 , ALA B:280 , ALA B:281 , LEU B:284
BINDING SITE FOR RESIDUE GOL A 7
4
AC4
SOFTWARE
SO4 A:4
BINDING SITE FOR RESIDUE NH4 A 8
5
AC5
SOFTWARE
HOH B:10 , HOH B:25 , THR B:317 , ARG B:320
BINDING SITE FOR RESIDUE SO4 B 1
6
AC6
SOFTWARE
ARG A:310 , LYS B:294
BINDING SITE FOR RESIDUE SO4 B 3
7
AC7
SOFTWARE
SER A:261 , LYS A:262 , THR A:317 , ARG A:320 , ARG A:321 , LYS B:262
BINDING SITE FOR RESIDUE GOL B 5
8
AC8
SOFTWARE
LYS A:313 , LYS B:262 , TRP B:290
BINDING SITE FOR RESIDUE GOL B 6
[
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
(2, 4)
Info
All Exons
Exon 1.6 (A:261-294 | B:262-294)
Exon 1.7a (A:295-335 | B:295-334)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.5b/1.6
2: Boundary 1.6/1.7a
3: Boundary 1.7a/1.8a
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
1.3d
ENST00000224237
3d
ENSE00002186269
chr10:
17271277-17271984
708
VIME_HUMAN
1-188
188
0
-
-
1.4c
ENST00000224237
4c
ENSE00001270958
chr10:
17272649-17272709
61
VIME_HUMAN
188-208
21
0
-
-
1.5b
ENST00000224237
5b
ENSE00000692805
chr10:
17275586-17275681
96
VIME_HUMAN
209-240
32
0
-
-
1.6
ENST00000224237
6
ENSE00000692809
chr10:
17275769-17275930
162
VIME_HUMAN
241-294
54
2
A:261-294
B:262-294
34
33
1.7a
ENST00000224237
7a
ENSE00000692812
chr10:
17276692-17276817
126
VIME_HUMAN
295-336
42
2
A:295-335
B:295-334
41
40
1.8a
ENST00000224237
8a
ENSE00001270949
chr10:
17277168-17277388
221
VIME_HUMAN
337-410
74
0
-
-
1.8c
ENST00000224237
8c
ENSE00001121153
chr10:
17277845-17277888
44
VIME_HUMAN
410-425
16
0
-
-
1.8e
ENST00000224237
8e
ENSE00000815998
chr10:
17278293-17278378
86
VIME_HUMAN
425-453
29
0
-
-
1.9
ENST00000224237
9
ENSE00001906870
chr10:
17279229-17279592
364
VIME_HUMAN
454-466
13
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 (58 KB)
Header - Asym.Unit
Biol.Unit 1 (52 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
3TRT
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
