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2QQB
Biol. Unit 1
Info
Asym.Unit (42 KB)
Biol.Unit 1 (72 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DTXR(M10A C102D) COMPLEXED WITH NICKEL(II)
Authors
:
J. A. D'Aquino, J. R. Lattimer, A. Denninger, K. E. D'Aquino, D. Ringe
Date
:
26 Jul 07 (Deposition) - 30 Oct 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.92
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Repressor, Regulator, Dtxr, Helix-Turn-Helix, Metal Ion, Activation, Dna-Binding, Ferrous Iron, Cytoplasm, Transcription, Transcription Regulation, Transcription Regulator
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. A. D'Aquino, J. R. Lattimer, A. Denninger, K. E. D'Aquino, D. Ringe
Role Of The N-Terminal Helix In The Metal Ion-Induced Activation Of The Diphtheria Toxin Repressor Dtxr.
Biochemistry V. 46 11761 2007
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: NICKEL (II) ION (NIa)
1b: NICKEL (II) ION (NIb)
2a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NI
-1
Ligand/Ion
NICKEL (II) ION
2
PO4
2
Ligand/Ion
PHOSPHATE ION
[
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]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:79 , GLU A:83 , HIS A:98 , PO4 A:600 , HOH A:613
BINDING SITE FOR RESIDUE NI A 551
2
AC2
SOFTWARE
ASP A:102 , GLU A:105 , HIS A:106 , HOH A:608 , HOH A:612
BINDING SITE FOR RESIDUE NI A 552
3
AC3
SOFTWARE
HIS A:79 , ARG A:80 , GLU A:83 , SER A:126 , PHE A:128 , ASN A:130 , NI A:551 , HOH A:613
BINDING SITE FOR RESIDUE PO4 A 600
[
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]
SAPs(SNPs)/Variants
(11, 22)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_DTXR_CORDI_001 (R47H, chain A, )
02: VAR_DTXR_CORDI_004 (I165V, chain A, )
03: VAR_DTXR_CORDI_005 (V174A, chain A, )
04: VAR_DTXR_CORDI_006 (S191T, chain A, )
05: VAR_DTXR_CORDI_008 (H201R, chain A, )
06: VAR_DTXR_CORDI_009 (S205R, chain A, )
07: VAR_DTXR_CORDI_010 (L214L, chain A, )
08: VAR_DTXR_CORDI_011 (L214Y, chain A, )
09: VAR_DTXR_CORDI_012 (A218T, chain A, )
10: VAR_DTXR_CORDI_013 (I221M, chain A, )
11: VAR_DTXR_CORDI_014 (I221T, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_DTXR_CORDI_001
*
R
47
H
DTXR_CORDI
---
---
A
R
47
H
02
UniProt
VAR_DTXR_CORDI_004
*
I
165
V
DTXR_CORDI
---
---
A
I
165
V
03
UniProt
VAR_DTXR_CORDI_005
*
V
174
A
DTXR_CORDI
---
---
A
V
174
A
04
UniProt
VAR_DTXR_CORDI_006
*
S
191
T
DTXR_CORDI
---
---
A
S
191
T
05
UniProt
VAR_DTXR_CORDI_008
*
H
201
R
DTXR_CORDI
---
---
A
H
201
R
06
UniProt
VAR_DTXR_CORDI_009
*
S
205
R
DTXR_CORDI
---
---
A
S
205
R
07
UniProt
VAR_DTXR_CORDI_010
*
I
214
L
DTXR_CORDI
---
---
A
L
214
L
08
UniProt
VAR_DTXR_CORDI_011
*
I
214
Y
DTXR_CORDI
---
---
A
L
214
Y
09
UniProt
VAR_DTXR_CORDI_012
*
A
218
T
DTXR_CORDI
---
---
A
A
218
T
10
UniProt
VAR_DTXR_CORDI_013
*
I
221
M
DTXR_CORDI
---
---
A
I
221
M
11
UniProt
VAR_DTXR_CORDI_014
*
I
221
T
DTXR_CORDI
---
---
A
I
221
T
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: HTH_DTXR (A:4-65)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HTH_DTXR
PS50944
DtxR-type HTH domain profile.
DTXR_CORDI
4-65
2
A:4-65
DTXR_CORDW
4-65
2
A:4-65
[
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Exons
(0, 0)
Info
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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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2qqba1 (A:3-64)
2a: SCOP_d2qqba2 (A:65-139)
3a: SCOP_d2qqba3 (A:149-226)
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Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Winged helix DNA-binding domain
(576)
Family
:
Iron-dependent repressor protein
(44)
Protein domain
:
Diphtheria toxin repressor (DtxR)
(20)
Corynebacterium diphtheriae [TaxId: 1717]
(20)
1a
d2qqba1
A:3-64
Fold
:
Iron-dependent repressor protein, dimerization domain
(45)
Superfamily
:
Iron-dependent repressor protein, dimerization domain
(45)
Family
:
Iron-dependent repressor protein, dimerization domain
(44)
Protein domain
:
Diphtheria toxin repressor (DtxR)
(20)
Corynebacterium diphtheriae [TaxId: 1717]
(20)
2a
d2qqba2
A:65-139
Class
:
All beta proteins
(24004)
Fold
:
SH3-like barrel
(1035)
Superfamily
:
C-terminal domain of transcriptional repressors
(56)
Family
:
FeoA-like
(23)
Protein domain
:
Diphtheria toxin repressor (DtxR)
(18)
Corynebacterium diphtheriae [TaxId: 1717]
(18)
3a
d2qqba3
A:149-226
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Fe_dep_repr_C_2qqbA01 (A:65-135)
2a: PFAM_Fe_dep_repress_2qqbA02 (A:3-62)
3a: PFAM_FeoA_2qqbA03 (A:155-225)
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Clan
:
HTH
(544)
Family
:
Fe_dep_repr_C
(11)
Corynebacterium diphtheriae
(7)
1a
Fe_dep_repr_C-2qqbA01
A:65-135
Family
:
Fe_dep_repress
(10)
Corynebacterium diphtheriae
(6)
2a
Fe_dep_repress-2qqbA02
A:3-62
Clan
:
TRB
(15)
Family
:
FeoA
(11)
Corynebacterium diphtheriae
(6)
3a
FeoA-2qqbA03
A:155-225
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