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.
1TJL
Biol. Unit 3
Info
Asym.Unit (265 KB)
Biol.Unit 1 (29 KB)
Biol.Unit 10 (29 KB)
Biol.Unit 11 (54 KB)
Biol.Unit 2 (29 KB)
Biol.Unit 3 (28 KB)
Biol.Unit 4 (29 KB)
Biol.Unit 5 (28 KB)
Biol.Unit 6 (29 KB)
Biol.Unit 7 (29 KB)
Biol.Unit 8 (28 KB)
Biol.Unit 9 (28 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 TRANSCRIPTION FACTOR DKSA FROM E. COLI
Authors
:
A. Perederina, V. Svetlov, M. N. Vassylyeva, I. Artsimovitch, S. Yokoy D. G. Vassylyev, Riken Structural Genomics/Proteomics Initiati
Date
:
06 Jun 04 (Deposition) - 07 Sep 04 (Release) - 16 Apr 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Biol. Unit 9: I (1x)
Biol. Unit 10: J (1x)
Biol. Unit 11: A,C (1x)
Keywords
:
Dksa, Transcription Factor, Rna Polymerase, Stringent Response, Ppgpp, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transcription
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Perederina, V. Svetlov, M. N. Vassylyeva, T. H. Tahirov, S. Yokoyama, I. Artsimovitch, D. G. Vassylyev
Regulation Through The Secondary Channel--Structural Framework For Ppgpp-Dksa Synergism During Transcription
Cell(Cambridge, Mass. ) V. 118 297 2004
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: ZINC ION (ZNa)
1b: ZINC ION (ZNb)
1c: ZINC ION (ZNc)
1d: ZINC ION (ZNd)
1e: ZINC ION (ZNe)
1f: ZINC ION (ZNf)
1g: ZINC ION (ZNg)
1h: ZINC ION (ZNh)
1i: ZINC ION (ZNi)
1j: ZINC ION (ZNj)
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(1, 1)
Info
All Sites
1: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
CYS C:114 , CYS C:117 , CYS C:135 , CYS C:138
BINDING SITE FOR RESIDUE ZN C 200
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: ZF_DKSA_2 (C:71-151)
2: ZF_DKSA_1 (C:114-138)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZF_DKSA_2
PS51128
Prokaryotic dksA C4-type zinc finger profiles.
DKSA_ECOLI
71-151
1
-
-
C:71-151
-
-
-
-
-
-
-
2
ZF_DKSA_1
PS01102
Prokaryotic dksA C4-type zinc finger.
DKSA_ECOLI
114-138
1
-
-
C:114-138
-
-
-
-
-
-
-
[
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, 20)
Info
All SCOP Domains
1a: SCOP_d1tjla1 (A:7-110)
1b: SCOP_d1tjlb1 (B:7-110)
1c: SCOP_d1tjlc1 (C:7-110)
1d: SCOP_d1tjld1 (D:7-110)
1e: SCOP_d1tjle1 (E:7-110)
1f: SCOP_d1tjlf1 (F:7-110)
1g: SCOP_d1tjlg1 (G:7-110)
1h: SCOP_d1tjlh1 (H:7-110)
1i: SCOP_d1tjli1 (I:7-110)
1j: SCOP_d1tjlj1 (J:7-110)
2a: SCOP_d1tjla2 (A:111-151)
2b: SCOP_d1tjlb2 (B:111-151)
2c: SCOP_d1tjlc2 (C:111-151)
2d: SCOP_d1tjld2 (D:111-151)
2e: SCOP_d1tjle2 (E:111-151)
2f: SCOP_d1tjlf2 (F:111-151)
2g: SCOP_d1tjlg2 (G:111-151)
2h: SCOP_d1tjlh2 (H:111-151)
2i: SCOP_d1tjli2 (I:111-151)
2j: SCOP_d1tjlj2 (J:111-151)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Long alpha-hairpin
(315)
Superfamily
:
DnaK suppressor protein DksA, alpha-hairpin domain
(1)
Family
:
DnaK suppressor protein DksA, alpha-hairpin domain
(1)
Protein domain
:
DnaK suppressor protein DksA, alpha-hairpin domain
(1)
Escherichia coli [TaxId: 562]
(1)
1a
d1tjla1
A:7-110
1b
d1tjlb1
B:7-110
1c
d1tjlc1
C:7-110
1d
d1tjld1
D:7-110
1e
d1tjle1
E:7-110
1f
d1tjlf1
F:7-110
1g
d1tjlg1
G:7-110
1h
d1tjlh1
H:7-110
1i
d1tjli1
I:7-110
1j
d1tjlj1
J:7-110
Class
:
Small proteins
(3458)
Fold
:
Glucocorticoid receptor-like (DNA-binding domain)
(292)
Superfamily
:
Glucocorticoid receptor-like (DNA-binding domain)
(292)
Family
:
Prokaryotic DksA/TraR C4-type zinc finger
(1)
Protein domain
:
DnaK suppressor protein DksA, zinc finger domain
(1)
Escherichia coli [TaxId: 562]
(1)
2a
d1tjla2
A:111-151
2b
d1tjlb2
B:111-151
2c
d1tjlc2
C:111-151
2d
d1tjld2
D:111-151
2e
d1tjle2
E:111-151
2f
d1tjlf2
F:111-151
2g
d1tjlg2
G:111-151
2h
d1tjlh2
H:111-151
2i
d1tjli2
I:111-151
2j
d1tjlj2
J:111-151
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 10)
Info
all PFAM domains
1a: PFAM_zf_dskA_traR_1tjlJ01 (J:109-147)
1b: PFAM_zf_dskA_traR_1tjlJ02 (J:109-147)
1c: PFAM_zf_dskA_traR_1tjlJ03 (J:109-147)
1d: PFAM_zf_dskA_traR_1tjlJ04 (J:109-147)
1e: PFAM_zf_dskA_traR_1tjlJ05 (J:109-147)
1f: PFAM_zf_dskA_traR_1tjlJ06 (J:109-147)
1g: PFAM_zf_dskA_traR_1tjlJ07 (J:109-147)
1h: PFAM_zf_dskA_traR_1tjlJ08 (J:109-147)
1i: PFAM_zf_dskA_traR_1tjlJ09 (J:109-147)
1j: PFAM_zf_dskA_traR_1tjlJ10 (J:109-147)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Zn_Beta_Ribbon
(109)
Family
:
zf-dskA_traR
(2)
Escherichia coli (strain K12)
(2)
1a
zf-dskA_traR-1tjlJ01
J:109-147
1b
zf-dskA_traR-1tjlJ02
J:109-147
1c
zf-dskA_traR-1tjlJ03
J:109-147
1d
zf-dskA_traR-1tjlJ04
J:109-147
1e
zf-dskA_traR-1tjlJ05
J:109-147
1f
zf-dskA_traR-1tjlJ06
J:109-147
1g
zf-dskA_traR-1tjlJ07
J:109-147
1h
zf-dskA_traR-1tjlJ08
J:109-147
1i
zf-dskA_traR-1tjlJ09
J:109-147
1j
zf-dskA_traR-1tjlJ10
J:109-147
[
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
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 (265 KB)
Header - Asym.Unit
Biol.Unit 1 (29 KB)
Header - Biol.Unit 1
Biol.Unit 10 (29 KB)
Header - Biol.Unit 10
Biol.Unit 11 (54 KB)
Header - Biol.Unit 11
Biol.Unit 2 (29 KB)
Header - Biol.Unit 2
Biol.Unit 3 (28 KB)
Header - Biol.Unit 3
Biol.Unit 4 (29 KB)
Header - Biol.Unit 4
Biol.Unit 5 (28 KB)
Header - Biol.Unit 5
Biol.Unit 6 (29 KB)
Header - Biol.Unit 6
Biol.Unit 7 (29 KB)
Header - Biol.Unit 7
Biol.Unit 8 (28 KB)
Header - Biol.Unit 8
Biol.Unit 9 (28 KB)
Header - Biol.Unit 9
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
1TJL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help