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.
2VV5
Asym. Unit
Info
Asym.Unit (277 KB)
Biol.Unit 1 (269 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE OPEN STRUCTURE OF MSCS
Authors
:
W. Wang, C. Dong, K. A. Johnson, J. H. Naismith
Date
:
03 Jun 08 (Deposition) - 05 Aug 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.45
Chains
:
Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A,B,C,D,E,F,G (1x)
Keywords
:
Ion Transport, Transmembrane, Inner Membrane, Membrane Structure, Membrane Protein, Membrane, Transport, Open Channel, Ionic Channel
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Wang, S. S. Black, M. D. Edwards, S. Miller, E. L. Morrison, W. Bartlett, C. Dong, J. H. Naismith, I. R. Booth
The Structure Of An Open Form Of An E. Coli Mechanosensitive Channel At 3. 45 A Resolution.
Science V. 321 1179 2008
[
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
(1, 7)
Info
All PROSITE Patterns/Profiles
1: UPF0003 (A:143-177,B:143-177,C:143-177,D:14...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UPF0003
PS01246
Uncharacterized protein family UPF0003 signature.
MSCS_ECO57
143-177
7
A:143-177
B:143-177
C:143-177
D:143-177
E:143-177
F:143-177
G:143-177
MSCS_ECOLI
143-177
7
A:143-177
B:143-177
C:143-177
D:143-177
E:143-177
F:143-177
G:143-177
[
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.
SCOP Domains
(3, 21)
Info
All SCOP Domains
1a: SCOP_d2vv5a1 (A:113-179)
1b: SCOP_d2vv5b1 (B:113-179)
1c: SCOP_d2vv5c1 (C:113-179)
1d: SCOP_d2vv5d1 (D:113-179)
1e: SCOP_d2vv5e1 (E:113-179)
1f: SCOP_d2vv5f1 (F:113-179)
1g: SCOP_d2vv5g1 (G:113-179)
2a: SCOP_d2vv5a2 (A:180-280)
2b: SCOP_d2vv5b2 (B:180-280)
2c: SCOP_d2vv5c2 (C:180-280)
2d: SCOP_d2vv5d2 (D:180-280)
2e: SCOP_d2vv5e2 (E:180-280)
2f: SCOP_d2vv5f2 (F:180-280)
2g: SCOP_d2vv5g2 (G:180-280)
3a: SCOP_d2vv5a3 (A:27-112)
3b: SCOP_d2vv5b3 (B:27-112)
3c: SCOP_d2vv5c3 (C:27-112)
3d: SCOP_d2vv5d3 (D:27-112)
3e: SCOP_d2vv5e3 (E:27-112)
3f: SCOP_d2vv5f3 (F:27-112)
3g: SCOP_d2vv5g3 (G:27-112)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Sm-like fold
(103)
Superfamily
:
Sm-like ribonucleoproteins
(95)
Family
:
Mechanosensitive channel protein MscS (YggB), middle domain
(2)
Protein domain
:
Mechanosensitive channel protein MscS (YggB), middle domain
(2)
Escherichia coli [TaxId: 562]
(2)
1a
d2vv5a1
A:113-179
1b
d2vv5b1
B:113-179
1c
d2vv5c1
C:113-179
1d
d2vv5d1
D:113-179
1e
d2vv5e1
E:113-179
1f
d2vv5f1
F:113-179
1g
d2vv5g1
G:113-179
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Mechanosensitive channel protein MscS (YggB), C-terminal domain
(2)
Family
:
Mechanosensitive channel protein MscS (YggB), C-terminal domain
(2)
Protein domain
:
Mechanosensitive channel protein MscS (YggB), C-terminal domain
(2)
Escherichia coli [TaxId: 562]
(2)
2a
d2vv5a2
A:180-280
2b
d2vv5b2
B:180-280
2c
d2vv5c2
C:180-280
2d
d2vv5d2
D:180-280
2e
d2vv5e2
E:180-280
2f
d2vv5f2
F:180-280
2g
d2vv5g2
G:180-280
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Mechanosensitive channel protein MscS (YggB), transmembrane region
(2)
Superfamily
:
Mechanosensitive channel protein MscS (YggB), transmembrane region
(2)
Family
:
Mechanosensitive channel protein MscS (YggB), transmembrane region
(2)
Protein domain
:
Mechanosensitive channel protein MscS (YggB), transmembrane region
(2)
Escherichia coli [TaxId: 562]
(2)
3a
d2vv5a3
A:27-112
3b
d2vv5b3
B:27-112
3c
d2vv5c3
C:27-112
3d
d2vv5d3
D:27-112
3e
d2vv5e3
E:27-112
3f
d2vv5f3
F:27-112
3g
d2vv5g3
G:27-112
[
close SCOP info
]
CATH Domains
(2, 14)
Info
all CATH domains
1a: CATH_2vv5A03 (A:179-273)
1b: CATH_2vv5B03 (B:179-273)
1c: CATH_2vv5C03 (C:179-273)
1d: CATH_2vv5D03 (D:179-273)
1e: CATH_2vv5E03 (E:179-273)
1f: CATH_2vv5F03 (F:179-273)
1g: CATH_2vv5G03 (G:179-273)
2a: CATH_2vv5A02 (A:129-178)
2b: CATH_2vv5B02 (B:129-178)
2c: CATH_2vv5C02 (C:129-178)
2d: CATH_2vv5D02 (D:129-178)
2e: CATH_2vv5E02 (E:129-178)
2f: CATH_2vv5F02 (F:129-178)
2g: CATH_2vv5G02 (G:129-178)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.100, no name defined]
(82)
Escherichia coli. Organism_taxid: 562.
(2)
1a
2vv5A03
A:179-273
1b
2vv5B03
B:179-273
1c
2vv5C03
C:179-273
1d
2vv5D03
D:179-273
1e
2vv5E03
E:179-273
1f
2vv5F03
F:179-273
1g
2vv5G03
G:179-273
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
SH3 type barrels.
(648)
Homologous Superfamily
:
[code=2.30.30.60, no name defined]
(9)
Escherichia coli. Organism_taxid: 562.
(1)
2a
2vv5A02
A:129-178
2b
2vv5B02
B:129-178
2c
2vv5C02
C:129-178
2d
2vv5D02
D:129-178
2e
2vv5E02
E:129-178
2f
2vv5F02
F:129-178
2g
2vv5G02
G:129-178
[
close CATH info
]
Pfam Domains
(2, 14)
Info
all PFAM domains
1a: PFAM_MS_channel_2vv5G01 (G:70-268)
1b: PFAM_MS_channel_2vv5G02 (G:70-268)
1c: PFAM_MS_channel_2vv5G03 (G:70-268)
1d: PFAM_MS_channel_2vv5G04 (G:70-268)
1e: PFAM_MS_channel_2vv5G05 (G:70-268)
1f: PFAM_MS_channel_2vv5G06 (G:70-268)
1g: PFAM_MS_channel_2vv5G07 (G:70-268)
2a: PFAM_TM_helix_2vv5G08 (G:25-66)
2b: PFAM_TM_helix_2vv5G09 (G:25-66)
2c: PFAM_TM_helix_2vv5G10 (G:25-66)
2d: PFAM_TM_helix_2vv5G11 (G:25-66)
2e: PFAM_TM_helix_2vv5G12 (G:25-66)
2f: PFAM_TM_helix_2vv5G13 (G:25-66)
2g: PFAM_TM_helix_2vv5G14 (G:25-66)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: MS_channel]
(2)
Family
:
MS_channel
(2)
Escherichia coli O157:H7
(1)
1a
MS_channel-2vv5G01
G:70-268
1b
MS_channel-2vv5G02
G:70-268
1c
MS_channel-2vv5G03
G:70-268
1d
MS_channel-2vv5G04
G:70-268
1e
MS_channel-2vv5G05
G:70-268
1f
MS_channel-2vv5G06
G:70-268
1g
MS_channel-2vv5G07
G:70-268
Clan
:
no clan defined [family: TM_helix]
(2)
Family
:
TM_helix
(2)
Escherichia coli O157:H7
(1)
2a
TM_helix-2vv5G08
G:25-66
2b
TM_helix-2vv5G09
G:25-66
2c
TM_helix-2vv5G10
G:25-66
2d
TM_helix-2vv5G11
G:25-66
2e
TM_helix-2vv5G12
G:25-66
2f
TM_helix-2vv5G13
G:25-66
2g
TM_helix-2vv5G14
G:25-66
[
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 C
Chain D
Chain E
Chain F
Chain G
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 (277 KB)
Header - Asym.Unit
Biol.Unit 1 (269 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
2VV5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
