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.
2IVZ
Biol. Unit 3
Info
Asym.Unit (281 KB)
Biol.Unit 1 (73 KB)
Biol.Unit 2 (74 KB)
Biol.Unit 3 (73 KB)
Biol.Unit 4 (72 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF TOLB IN COMPLEX WITH A PEPTIDE OF THE COLICIN E9 T-DOMAIN
Authors
:
S. R. Loftus, D. Walker, M. J. Mate, D. A. Bonsor, R. James, G. R. Moore, C. Kleanthous
Date
:
23 Jun 06 (Deposition) - 16 Aug 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E (1x)
Biol. Unit 2: B,F (1x)
Biol. Unit 3: C,G (1x)
Biol. Unit 4: D,H (1x)
Keywords
:
Protein Transport/Hydrolase, Protein-Protein Interaction, Protein Transport, Bacteriocin Transport, Tolb, Colicin, Plasmid, Nuclease, Hydrolase, Transport, Antibiotic, Periplasmic, Bacteriocin, Natively Disordered Proteins, Protein Transport/Hydrolase Complex, Endonuclease, Antimicrobial, Translocation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. R. Loftus, D. Walker, M. J. Mate, D. A. Bonsor, R. James, G. R. Moore, C. Kleanthous
Competitive Recruitment Of The Periplasmic Translocation Portal Tolb By A Natively Disordered Domain Of Colicin E9
Proc. Natl. Acad. Sci. Usa V. 103 12353 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(2, 2)
Info
All Sites
1: AC4 (SOFTWARE)
2: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
ASP C:337 , HOH C:2054 , HOH C:2238 , HOH C:2239 , HOH C:2241 , HOH C:2242 , HOH C:2272 , HOH C:2273
BINDING SITE FOR RESIDUE CA C1432
2
AC5
SOFTWARE
ASP C:339 , VAL C:340 , HOH C:2070 , HOH C:2201 , HOH C:2203 , HOH C:2243 , HOH C:2244
BINDING SITE FOR RESIDUE CA C1433
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2ivza1 (A:163-431)
1b: SCOP_d2ivzb1 (B:163-431)
1c: SCOP_d2ivzc1 (C:163-431)
1d: SCOP_d2ivzd1 (D:163-431)
2a: SCOP_d2ivza2 (A:35-162)
2b: SCOP_d2ivzb2 (B:35-162)
2c: SCOP_d2ivzc2 (C:35-162)
2d: SCOP_d2ivzd2 (D:35-162)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
6-bladed beta-propeller
(327)
Superfamily
:
TolB, C-terminal domain
(7)
Family
:
TolB, C-terminal domain
(7)
Protein domain
:
TolB, C-terminal domain
(4)
Escherichia coli [TaxId: 562]
(4)
1a
d2ivza1
A:163-431
1b
d2ivzb1
B:163-431
1c
d2ivzc1
C:163-431
1d
d2ivzd1
D:163-431
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Anticodon-binding domain-like
(97)
Superfamily
:
TolB, N-terminal domain
(7)
Family
:
TolB, N-terminal domain
(4)
Protein domain
:
TolB, N-terminal domain
(4)
Escherichia coli [TaxId: 562]
(4)
2a
d2ivza2
A:35-162
2b
d2ivzb2
B:35-162
2c
d2ivzc2
C:35-162
2d
d2ivzd2
D:35-162
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2ivzD01 (D:34-165)
1b: CATH_2ivzA01 (A:35-165)
1c: CATH_2ivzB01 (B:35-165)
1d: CATH_2ivzC01 (C:35-165)
2a: CATH_2ivzA02 (A:166-431)
2b: CATH_2ivzB02 (B:166-431)
2c: CATH_2ivzC02 (C:166-431)
2d: CATH_2ivzD02 (D:166-431)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.10070, no name defined]
(6)
Escherichia coli. Organism_taxid: 562.
(4)
1a
2ivzD01
D:34-165
1b
2ivzA01
A:35-165
1c
2ivzB01
B:35-165
1d
2ivzC01
C:35-165
Class
:
Mainly Beta
(13760)
Architecture
:
6 Propellor
(215)
Topology
:
Neuraminidase
(215)
Homologous Superfamily
:
TolB, C-terminal domain
(42)
Escherichia coli. Organism_taxid: 562.
(4)
2a
2ivzA02
A:166-431
2b
2ivzB02
B:166-431
2c
2ivzC02
C:166-431
2d
2ivzD02
D:166-431
[
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 C
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 (281 KB)
Header - Asym.Unit
Biol.Unit 1 (73 KB)
Header - Biol.Unit 1
Biol.Unit 2 (74 KB)
Header - Biol.Unit 2
Biol.Unit 3 (73 KB)
Header - Biol.Unit 3
Biol.Unit 4 (72 KB)
Header - Biol.Unit 4
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
2IVZ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
