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.
2J80
Asym. Unit
Info
Asym.Unit (93 KB)
Biol.Unit 1 (87 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 CITRATE-BOUND PERIPLASMIC DOMAIN OF SENSOR HISTIDINE KINASE CITA
Authors
:
M. Sevvana, V. Vijayan, M. Zweckstetter, S. Reinelt, D. R. Madden, G. M. Sheldrick, M. Bott, C. Griesinger, S. Becker
Date
:
18 Oct 06 (Deposition) - 23 Oct 07 (Release) - 13 Apr 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Transferase, Signal Transduction, Transmembrane, Phosphorylation, Two-Component Regulatory System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Sevvana, V. Vijayan, M. Zweckstetter, S. Reinelt, D. R. Madden, R. Herbst-Irmer, G. M. Sheldrick, M. Bott, C. Griesinger, S. Becker
A Ligand-Induced Switch In The Periplasmic Domain Of Sensor Histidine Kinase Cita.
J. Mol. Biol. V. 377 512 2008
[
close entry info
]
Hetero Components
(5, 15)
Info
All Hetero Components
1a: CITRATE ANION (FLCa)
1b: CITRATE ANION (FLCb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FLC
2
Ligand/Ion
CITRATE ANION
2
GOL
2
Ligand/Ion
GLYCEROL
3
MSE
8
Mod. Amino Acid
SELENOMETHIONINE
4
NA
2
Ligand/Ion
SODIUM ION
5
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:56 , THR A:58 , ARG A:66 , HIS A:69 , MSE A:79 , GLU A:80 , GLY A:100 , SER A:101 , LEU A:102 , ARG A:107 , LYS A:109 , SER A:124 , HOH A:2087 , HOH A:2108
BINDING SITE FOR RESIDUE FLC A1133
2
AC2
SOFTWARE
SER A:24 , SER A:110 , PRO A:111 , GOL A:1136 , HOH A:2089
BINDING SITE FOR RESIDUE NA A1134
3
AC3
SOFTWARE
GLY A:103 , SER A:104 , HOH A:2086 , SER B:104
BINDING SITE FOR RESIDUE SO4 A1135
4
AC4
SOFTWARE
MSE A:21 , SER A:24 , SER A:93 , SER A:110 , NA A:1134 , HOH A:2091 , HOH A:2109 , HOH A:2110 , PHE B:51
BINDING SITE FOR RESIDUE GOL A1136
5
AC5
SOFTWARE
TYR B:56 , THR B:58 , ARG B:66 , HIS B:69 , MSE B:79 , GLU B:80 , GLY B:100 , SER B:101 , LEU B:102 , ARG B:107 , LYS B:109 , SER B:124 , HOH B:2084 , HOH B:2102
BINDING SITE FOR RESIDUE FLC B1130
6
AC6
SOFTWARE
SER B:24 , SER B:110 , PRO B:111 , GOL B:1132 , HOH B:2086
BINDING SITE FOR RESIDUE NA B1131
7
AC7
SOFTWARE
PHE A:51 , MSE B:21 , SER B:24 , SER B:93 , SER B:110 , NA B:1131 , HOH B:2078 , HOH B:2103 , HOH B:2104
BINDING SITE FOR RESIDUE GOL B1132
[
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
(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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2j80a_ (A:)
1b: SCOP_d2j80b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Profilin-like
(304)
Superfamily
:
Sensory domain-like
(15)
Family
:
Sensory domain of two-component sensor kinase
(5)
Protein domain
:
automated matches
(3)
Klebsiella pneumoniae [TaxId: 573]
(2)
1a
d2j80a_
A:
1b
d2j80b_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2j80B00 (B:6-129)
1b: CATH_2j80A00 (A:4-132)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Beta-Lactamase
(202)
Homologous Superfamily
:
[code=3.30.450.20, no name defined]
(117)
Klebsiella pneumoniae. Organism_taxid: 573.
(1)
1a
2j80B00
B:6-129
1b
2j80A00
A:4-132
[
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 (93 KB)
Header - Asym.Unit
Biol.Unit 1 (87 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
2J80
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help