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2HZV
Biol. Unit 1
Info
Asym.Unit (226 KB)
Biol.Unit 1 (111 KB)
Biol.Unit 2 (110 KB)
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(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
)
[
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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
[
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]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC1 (SOFTWARE)
7: BC8 (SOFTWARE)
8: BC9 (SOFTWARE)
9: CC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS B:87 , HIS B:89 , CYS B:95 , HIS D:76
BINDING SITE FOR RESIDUE NI D 301
2
AC2
SOFTWARE
HIS A:87 , VAL A:88 , HIS A:89 , CYS A:95 , VAL C:72 , HIS C:76
BINDING SITE FOR RESIDUE NI A 302
3
AC3
SOFTWARE
HIS A:76 , HIS C:87 , VAL C:88 , HIS C:89 , CYS C:95
BINDING SITE FOR RESIDUE NI C 303
4
AC4
SOFTWARE
VAL B:72 , HIS B:76 , HIS D:87 , HIS D:89 , CYS D:95
BINDING SITE FOR RESIDUE NI D 304
5
AC9
SOFTWARE
GLU A:30 , ASP A:34 , ILE B:116 , GLN B:118 , VAL B:121
BINDING SITE FOR RESIDUE K A 401
6
BC1
SOFTWARE
GLU C:30 , ASP C:34 , ILE D:116 , ALA D:117 , GLN D:118 , VAL D:121
BINDING SITE FOR RESIDUE K C 402
7
BC8
SOFTWARE
HIS A:79 , SER A:82 , HIS C:89
BINDING SITE FOR RESIDUE K A 409
8
BC9
SOFTWARE
HIS B:79 , SER B:82 , HIS D:89
BINDING SITE FOR RESIDUE K B 410
9
CC1
SOFTWARE
HIS A:89 , HIS C:79 , SER C:82
BINDING SITE FOR RESIDUE K C 411
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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:
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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:
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)
(
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(
)
(
)
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
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Protein & NOT PROSITE
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Chain B
Chain C
Chain D
Chain I
Chain J
Asymmetric Unit 1
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Asym.Unit (226 KB)
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