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2CAD
Biol. Unit 1
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Asym.Unit (54 KB)
Biol.Unit 1 (95 KB)
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(1)
Title
:
NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION AND NICKEL BOUND TO 2F, 2X AND 2I SITES.
Authors
:
C. Dian, K. Schauer, U. Kapp, S. M. Mcsweeney, A. Labigne, L. Terradot
Date
:
20 Dec 05 (Deposition) - 17 Jul 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Nickel Uptake, Transcription Regulator, Ribbon-Helix-Helix, Acidic-Adaptive Response, Transcriptional Regulation, Dna- Binding, Hypothetical Protein, Metal-Binding, Nickel
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
C. Dian, K. Schauer, U. Kapp, S. M. Mcsweeney, A. Labigne, L. Terradot
Structural Basis Of The Nickel Response In Helicobacter Pylori: Crystal Structures Of Hpnikr In Apo And Nickel-Bound States.
J. Mol. Biol. V. 361 715 2006
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Hetero Components
(3, 16)
Info
All Hetero Components
1a: CITRIC ACID (CITa)
2a: FORMIC ACID (FMTa)
2b: FORMIC ACID (FMTb)
2c: FORMIC ACID (FMTc)
2d: FORMIC ACID (FMTd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
4a: NICKEL (II) ION (NIa)
4b: NICKEL (II) ION (NIb)
4c: NICKEL (II) ION (NIc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CIT
2
Ligand/Ion
CITRIC ACID
2
FMT
8
Ligand/Ion
FORMIC ACID
3
GOL
6
Ligand/Ion
GLYCEROL
4
NI
-1
Ligand/Ion
NICKEL (II) ION
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Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:74 , HIS A:101 , HOH A:2022 , HOH A:2062 , HIS B:88 , HOH B:2028
BINDING SITE FOR RESIDUE NI A1152
02
AC2
SOFTWARE
ILE A:84 , HIS A:88 , HIS B:99 , HIS B:101 , CYS B:107
BINDING SITE FOR RESIDUE NI B1151
03
AC3
SOFTWARE
HIS B:74 , HIS B:75 , GLU B:104 , CIT B:1150
BINDING SITE FOR RESIDUE NI B1152
04
AC4
SOFTWARE
HIS A:88 , ALA A:89 , HOH A:2029 , HIS B:74 , HIS B:75 , GLU B:104 , GOL B:1148 , NI B:1152 , HOH B:2055
BINDING SITE FOR RESIDUE CIT B1150
05
AC5
SOFTWARE
ILE A:84 , GLN A:87 , THR A:97 , HIS A:99 , GLU A:109 , HOH A:2060 , HIS B:99
BINDING SITE FOR RESIDUE FMT A1147
06
AC6
SOFTWARE
ALA A:136
BINDING SITE FOR RESIDUE FMT A1148
07
AC7
SOFTWARE
GLN A:76 , ARG A:82 , ARG A:131 , FMT A:1150
BINDING SITE FOR RESIDUE FMT A1149
08
AC8
SOFTWARE
ARG A:82 , LEU A:130 , ARG A:131 , FMT A:1149 , HOH A:2061
BINDING SITE FOR RESIDUE FMT A1150
09
AC9
SOFTWARE
TYR A:72 , ASN A:80 , HIS A:99 , HOH A:2062 , HOH A:2063 , GOL B:1149 , HOH B:2028
BINDING SITE FOR RESIDUE GOL A1151
10
BC1
SOFTWARE
HIS B:75 , HIS B:105 , CIT B:1150
BINDING SITE FOR RESIDUE GOL B1148
11
BC2
SOFTWARE
GOL A:1151 , ASN B:80 , MET B:83 , GLN B:87 , THR B:97 , GLU B:109 , HOH B:2054
BINDING SITE FOR RESIDUE GOL B1149
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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)
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Exons
(0, 0)
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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, 4)
Info
All SCOP Domains
1a: SCOP_d2cada1 (A:9-60)
1b: SCOP_d2cadb1 (B:9-57)
2a: SCOP_d2cada2 (A:61-146)
2b: SCOP_d2cadb2 (B:62-147)
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Protein Domains
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Organisms
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Class
:
All alpha proteins
(14657)
Fold
:
Ribbon-helix-helix
(65)
Superfamily
:
Ribbon-helix-helix
(65)
Family
:
automated matches
(13)
Protein domain
:
automated matches
(13)
Helicobacter pylori [TaxId: 85962]
(9)
1a
d2cada1
A:9-60
1b
d2cadb1
B:9-57
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
ACT-like
(63)
Family
:
automated matches
(16)
Protein domain
:
automated matches
(16)
Helicobacter pylori [TaxId: 85962]
(9)
2a
d2cada2
A:61-146
2b
d2cadb2
B:62-147
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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