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.
1JE8
Biol. Unit 2
Info
Asym.Unit (91 KB)
Biol.Unit 1 (44 KB)
Biol.Unit 2 (44 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
TWO-COMPONENT RESPONSE REGULATOR NARL/DNA COMPLEX: DNA BENDING FOUND IN A HIGH AFFINITY SITE
Authors
:
A. E. Maris, M. R. Sawaya, M. Kaczor-Grzeskowiak, M. R. Jarvis, S. M. D. Bearson, M. L. Kopka, I. Schroder, R. P. Gunsalus, R. E. Dickerson
Date
:
15 Jun 01 (Deposition) - 27 Sep 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.12
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Protein-Dna Complex, Two-Component Response Regulator, Helix-Turn-Helix, Dna Bending, Transcription/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. E. Maris, M. R. Sawaya, M. Kaczor-Grzeskowiak, M. R. Jarvis, S. M. Bearson, M. L. Kopka, I. Schroder, R. P. Gunsalus, R. E. Dickerson
Dimerization Allows Dna Target Site Recognition By The Narl Response Regulator.
Nat. Struct. Biol. V. 9 771 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 10)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
6
Mod. Amino Acid
SELENOMETHIONINE
2
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
SER E:185 , LYS E:188 , HOH E:413 , HOH E:419 , HOH E:423 , HOH E:424 , HOH G:29 , HOH G:31 , DC H:26 , HOH H:60
BINDING SITE FOR RESIDUE SO4 E 403
2
AC4
SOFTWARE
SER F:185 , LYS F:188 , HOH F:414 , HOH F:424 , HOH F:436 , DC G:5 , DC G:6 , HOH G:45 , HOH H:46 , HOH H:58
BINDING SITE FOR RESIDUE SO4 F 404
3
AC7
SOFTWARE
PRO E:158 , ARG E:161
BINDING SITE FOR RESIDUE SO4 E 407
4
AC8
SOFTWARE
PRO F:158 , ARG F:161
BINDING SITE FOR RESIDUE SO4 F 408
[
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
(1, 8)
Info
All PROSITE Patterns/Profiles
1: HTH_LUXR_1 (E:170-197,F:170-197)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HTH_LUXR_1
PS00622
LuxR-type HTH domain signature.
NARL_ECO57
170-197
2
-
-
E:170-197
F:170-197
NARL_ECOL6
170-197
2
-
-
E:170-197
F:170-197
NARL_ECOLI
170-197
2
-
-
E:170-197
F:170-197
NARL_SHIFL
170-197
2
-
-
E:170-197
F:170-197
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1je8a_ (A:)
1b: SCOP_d1je8b_ (B:)
1c: SCOP_d1je8e_ (E:)
1d: SCOP_d1je8f_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
C-terminal effector domain of the bipartite response regulators
(45)
Family
:
GerE-like (LuxR/UhpA family of transcriptional regulators)
(11)
Protein domain
:
Nitrate/nitrite response regulator (NarL)
(5)
Escherichia coli [TaxId: 562]
(5)
1a
d1je8a_
A:
1b
d1je8b_
B:
1c
d1je8e_
E:
1d
d1je8f_
F:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1je8E00 (E:150-216)
1b: CATH_1je8A00 (A:151-216)
1c: CATH_1je8B00 (B:151-216)
1d: CATH_1je8F00 (F:151-216)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
'winged helix' repressor DNA binding domain
(507)
[unclassified]
(77)
1a
1je8E00
E:150-216
1b
1je8A00
A:151-216
1c
1je8B00
B:151-216
1d
1je8F00
F:151-216
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_GerE_1je8F01 (F:153-210)
1b: PFAM_GerE_1je8F02 (F:153-210)
1c: PFAM_GerE_1je8F03 (F:153-210)
1d: PFAM_GerE_1je8F04 (F:153-210)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HTH
(544)
Family
:
GerE
(15)
Escherichia coli O157:H7
(1)
1a
GerE-1je8F01
F:153-210
1b
GerE-1je8F02
F:153-210
1c
GerE-1je8F03
F:153-210
1d
GerE-1je8F04
F:153-210
[
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 E
Chain F
Chain G
Chain H
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 (91 KB)
Header - Asym.Unit
Biol.Unit 1 (44 KB)
Header - Biol.Unit 1
Biol.Unit 2 (44 KB)
Header - Biol.Unit 2
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
1JE8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
