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2BJ7
Asym. Unit
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Asym.Unit (55 KB)
Biol.Unit 1 (97 KB)
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Title
:
NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES
Authors
:
T. H. Tahirov
Date
:
31 Jan 05 (Deposition) - 08 Apr 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Transcription, Repressor, Pyrococcus Horikoshii, Nikr, Dna- Binding, Metal-Binding, Nickel, Transcription Regulation, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. T. Chivers, T. H. Tahirov
Structure Of Pyrococcus Horikoshii Nikr: Nickel Sensing And Implications For The Regulation Of Dna Recognition
J. Mol. Biol. V. 348 597 2005
(for further references see the
PDB file header
)
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Hetero Components
(4, 9)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
3a: NICKEL (II) ION (NIa)
3b: NICKEL (II) ION (NIb)
3c: NICKEL (II) ION (NIc)
3d: NICKEL (II) ION (NId)
4a: TETRAETHYLENE GLYCOL (PG4a)
4b: TETRAETHYLENE GLYCOL (PG4b)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
NI
4
Ligand/Ion
NICKEL (II) ION
4
PG4
2
Ligand/Ion
TETRAETHYLENE GLYCOL
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:89 , HIS A:91 , CYS A:97 , HIS B:78
BINDING SITE FOR RESIDUE NI A1137
2
AC2
SOFTWARE
HOH A:2004 , ARG B:30 , HOH B:2023
BINDING SITE FOR RESIDUE CL B1139
3
AC3
SOFTWARE
LEU A:74 , HIS A:78 , HIS B:89 , HIS B:91 , CYS B:97
BINDING SITE FOR RESIDUE NI B1140
4
AC4
SOFTWARE
ASP A:75 , HIS B:64 , ASP B:65
BINDING SITE FOR RESIDUE NI B1141
5
AC5
SOFTWARE
HIS A:64 , ASP A:65 , HOH A:2024 , HOH A:2025 , ASP B:75
BINDING SITE FOR RESIDUE NI B1142
6
AC6
SOFTWARE
PHE A:6 , SER A:7 , HOH A:2053 , LYS B:127 , LEU B:128 , MET B:130
BINDING SITE FOR RESIDUE EDO A1138
7
AC7
SOFTWARE
HIS A:45 , LYS A:111 , ASP A:115 , LEU A:118 , HIS A:125 , GLY A:126 , HOH A:2043 , ILE B:25 , TYR B:27 , HOH B:2020
BINDING SITE FOR RESIDUE PG4 A1139
8
AC8
SOFTWARE
ASP A:19 , ILE A:22 , GLU A:23 , TYR A:27 , GLU A:28 , ARG A:30
BINDING SITE FOR RESIDUE PG4 A1140
9
AC9
SOFTWARE
MET A:1 , HIS B:125 , GLY B:126
BINDING SITE FOR RESIDUE EDO B1143
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2bj7a1 (A:1-50)
1b: SCOP_d2bj7b1 (B:1-50)
2a: SCOP_d2bj7a2 (A:51-137)
2b: SCOP_d2bj7b2 (B:51-138)
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)
Protein Domains
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)
(
)
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)
Pyrococcus horikoshii [TaxId: 53953]
(4)
1a
d2bj7a1
A:1-50
1b
d2bj7b1
B:1-50
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)
Pyrococcus horikoshii [TaxId: 53953]
(4)
2a
d2bj7a2
A:51-137
2b
d2bj7b2
B:51-138
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2bj7A01 (A:10-50)
1b: CATH_2bj7B01 (B:11-50)
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)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant
(30)
Homologous Superfamily
:
Met repressor-like
(30)
Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3.
(5)
1a
2bj7A01
A:10-50
1b
2bj7B01
B:11-50
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Pfam Domains
(0, 0)
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