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.
2HZV
Biol. Unit 2
Info
Asym.Unit (226 KB)
Biol.Unit 1 (111 KB)
Biol.Unit 2 (110 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
NIKR-OPERATOR DNA COMPLEX
Authors
:
E. R. Schreiter, C. L. Drennan
Date
:
09 Aug 06 (Deposition) - 22 Aug 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,I,J (1x)
Biol. Unit 2: E,F,G,H,K,L (1x)
Keywords
:
Nickel, Transcription Factor, Protein-Dna Complex, Ribbon- Helix-Helix, Metal Binding Protein/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. R. Schreiter, S. C. Wang, D. B. Zamble, C. L. Drennan
Nikr-Operator Complex Structure And The Mechanism Of Repressor Activation By Metal Ions.
Proc. Natl. Acad. Sci. Usa V. 103 13676 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 8)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
1e: POTASSIUM ION (Ke)
1f: POTASSIUM ION (Kf)
1g: POTASSIUM ION (Kg)
1h: POTASSIUM ION (Kh)
1i: POTASSIUM ION (Ki)
1j: POTASSIUM ION (Kj)
1k: POTASSIUM ION (Kk)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
3a: NICKEL (II) ION (NIa)
3b: NICKEL (II) ION (NIb)
3c: NICKEL (II) ION (NIc)
3d: NICKEL (II) ION (NId)
3e: NICKEL (II) ION (NIe)
3f: NICKEL (II) ION (NIf)
3g: NICKEL (II) ION (NIg)
3h: NICKEL (II) ION (NIh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
MSE
8
Mod. Amino Acid
SELENOMETHIONINE
3
NI
-1
Ligand/Ion
NICKEL (II) ION
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC2 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC5 (SOFTWARE)
09: BC6 (SOFTWARE)
10: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
HIS F:87 , HIS F:89 , CYS F:95 , VAL H:72 , HIS H:76
BINDING SITE FOR RESIDUE NI F 305
02
AC6
SOFTWARE
HIS E:87 , VAL E:88 , HIS E:89 , CYS E:95 , VAL G:72 , HIS G:76
BINDING SITE FOR RESIDUE NI E 306
03
AC7
SOFTWARE
VAL E:72 , HIS E:76 , HIS G:87 , HIS G:89 , CYS G:95
BINDING SITE FOR RESIDUE NI G 307
04
AC8
SOFTWARE
VAL F:72 , HIS F:76 , HIS H:87 , HIS H:89 , CYS H:95
BINDING SITE FOR RESIDUE NI H 308
05
BC2
SOFTWARE
GLU E:30 , ASP E:34 , ILE F:116 , ALA F:117 , GLN F:118 , VAL F:121
BINDING SITE FOR RESIDUE K E 403
06
BC3
SOFTWARE
GLU G:30 , ASP G:34 , ILE H:116 , ALA H:117 , GLN H:118 , VAL H:121
BINDING SITE FOR RESIDUE K G 404
07
BC4
SOFTWARE
HIS F:89 , HIS H:79 , SER H:82
BINDING SITE FOR RESIDUE K H 405
08
BC5
SOFTWARE
HIS E:79 , SER E:82 , HIS G:89
BINDING SITE FOR RESIDUE K E 406
09
BC6
SOFTWARE
HIS E:89 , HIS G:79 , SER G:82
BINDING SITE FOR RESIDUE K G 407
10
BC7
SOFTWARE
HIS F:79 , SER F:82 , HIS H:89
BINDING SITE FOR RESIDUE K 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
(, 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, 16)
Info
All SCOP Domains
1a: SCOP_d2hzva1 (A:1-48)
1b: SCOP_d2hzvc1 (C:1-48)
1c: SCOP_d2hzvd1 (D:1-48)
1d: SCOP_d2hzve1 (E:1-48)
1e: SCOP_d2hzvf1 (F:1-48)
1f: SCOP_d2hzvg1 (G:1-48)
1g: SCOP_d2hzvh1 (H:1-48)
1h: SCOP_d2hzvb1 (B:1-48)
2a: SCOP_d2hzva2 (A:49-131)
2b: SCOP_d2hzvb2 (B:49-131)
2c: SCOP_d2hzvc2 (C:49-131)
2d: SCOP_d2hzvd2 (D:49-131)
2e: SCOP_d2hzve2 (E:49-131)
2f: SCOP_d2hzvf2 (F:49-131)
2g: SCOP_d2hzvg2 (G:49-131)
2h: SCOP_d2hzvh2 (H:49-131)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ribbon-helix-helix
(65)
Superfamily
:
Ribbon-helix-helix
(65)
Family
:
CopG-like
(13)
Protein domain
:
Nickel responsive regulator NikR, N-terminal domain
(8)
Escherichia coli [TaxId: 562]
(4)
1a
d2hzva1
A:1-48
1b
d2hzvc1
C:1-48
1c
d2hzvd1
D:1-48
1d
d2hzve1
E:1-48
1e
d2hzvf1
F:1-48
1f
d2hzvg1
G:1-48
1g
d2hzvh1
H:1-48
1h
d2hzvb1
B:1-48
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
ACT-like
(63)
Family
:
Nickel responsive regulator NikR, C-terminal domain
(14)
Protein domain
:
Nickel responsive regulator NikR, C-terminal domain
(12)
Escherichia coli [TaxId: 562]
(8)
2a
d2hzva2
A:49-131
2b
d2hzvb2
B:49-131
2c
d2hzvc2
C:49-131
2d
d2hzvd2
D:49-131
2e
d2hzve2
E:49-131
2f
d2hzvf2
F:49-131
2g
d2hzvg2
G:49-131
2h
d2hzvh2
H:49-131
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_2hzvA02 (A:48-131)
1b: CATH_2hzvB02 (B:48-131)
1c: CATH_2hzvC02 (C:48-131)
1d: CATH_2hzvD02 (D:48-131)
1e: CATH_2hzvE02 (E:48-131)
1f: CATH_2hzvF02 (F:48-131)
1g: CATH_2hzvG02 (G:48-131)
1h: CATH_2hzvH02 (H:48-131)
2a: CATH_2hzvA01 (A:2-47)
2b: CATH_2hzvB01 (B:2-47)
2c: CATH_2hzvC01 (C:2-47)
2d: CATH_2hzvD01 (D:2-47)
2e: CATH_2hzvE01 (E:2-47)
2f: CATH_2hzvF01 (F:2-47)
2g: CATH_2hzvG01 (G:2-47)
2h: CATH_2hzvH01 (H:2-47)
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
:
ACT-like. Chain A, domain 2
(9)
[unclassified]
(1)
1a
2hzvA02
A:48-131
1b
2hzvB02
B:48-131
1c
2hzvC02
C:48-131
1d
2hzvD02
D:48-131
1e
2hzvE02
E:48-131
1f
2hzvF02
F:48-131
1g
2hzvG02
G:48-131
1h
2hzvH02
H:48-131
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant
(30)
Homologous Superfamily
:
Met repressor-like
(30)
[unclassified]
(5)
2a
2hzvA01
A:2-47
2b
2hzvB01
B:2-47
2c
2hzvC01
C:2-47
2d
2hzvD01
D:2-47
2e
2hzvE01
E:2-47
2f
2hzvF01
F:2-47
2g
2hzvG01
G:2-47
2h
2hzvH01
H:2-47
[
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 E
Chain F
Chain G
Chain H
Chain K
Chain L
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 (226 KB)
Header - Asym.Unit
Biol.Unit 1 (111 KB)
Header - Biol.Unit 1
Biol.Unit 2 (110 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
2HZV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help