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1DDN
Asym. Unit
Info
Asym.Unit (104 KB)
Biol.Unit 1 (96 KB)
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(1)
Title
:
DIPHTHERIA TOX REPRESSOR (C102D MUTANT)/TOX DNA OPERATOR COMPLEX
Authors
:
A. White, X. Ding, J. C. Vanderspek, J. R. Murphy, D. Ringe
Date
:
23 Jun 98 (Deposition) - 14 Oct 98 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Complex (Regulatory Protein/Dna), Diphtheria Tox Repressor, Transcription Regulation, Dna-Binding Regulatory Protein, Iron-Regulated Repressor, Dna- Protein, Dna-Repressor Complex, Gene Regulation/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. White, X. Ding, J. C. Vanderspek, J. R. Murphy, D. Ringe
Structure Of The Metal-Ion-Activated Diphtheria Toxin Repressor/Tox Operator Complex.
Nature V. 394 502 1998
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 8)
Info
All Hetero Components
1a: NICKEL (II) ION (NIa)
1b: NICKEL (II) ION (NIb)
1c: NICKEL (II) ION (NIc)
1d: NICKEL (II) ION (NId)
1e: NICKEL (II) ION (NIe)
1f: NICKEL (II) ION (NIf)
1g: NICKEL (II) ION (NIg)
1h: NICKEL (II) ION (NIh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NI
8
Ligand/Ion
NICKEL (II) ION
[
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]
Sites
(16, 16)
Info
All Sites
01: AA (UNKNOWN)
02: AC1 (SOFTWARE)
03: AC2 (SOFTWARE)
04: AC3 (SOFTWARE)
05: AC4 (SOFTWARE)
06: AC5 (SOFTWARE)
07: AC6 (SOFTWARE)
08: AC7 (SOFTWARE)
09: AC8 (SOFTWARE)
10: AP (UNKNOWN)
11: BA (UNKNOWN)
12: BP (UNKNOWN)
13: CA (UNKNOWN)
14: CP (UNKNOWN)
15: DA (UNKNOWN)
16: DP (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AA
UNKNOWN
NI A:251 , HIS A:79 , GLU A:83 , HIS A:98
NULL
02
AC1
SOFTWARE
HIS A:79 , GLU A:83 , HIS A:98
BINDING SITE FOR RESIDUE NI A 251
03
AC2
SOFTWARE
MET A:10 , ASP A:102 , GLU A:105 , HIS A:106 , HOH A:253
BINDING SITE FOR RESIDUE NI A 252
04
AC3
SOFTWARE
HIS B:79 , GLU B:83 , HIS B:98
BINDING SITE FOR RESIDUE NI B 251
05
AC4
SOFTWARE
MET B:10 , ASP B:102 , GLU B:105 , HIS B:106 , HOH B:253
BINDING SITE FOR RESIDUE NI B 252
06
AC5
SOFTWARE
HIS C:79 , GLU C:83 , HIS C:98
BINDING SITE FOR RESIDUE NI C 251
07
AC6
SOFTWARE
MET C:10 , ASP C:102 , GLU C:105 , HIS C:106 , HOH C:253
BINDING SITE FOR RESIDUE NI C 252
08
AC7
SOFTWARE
HIS D:79 , GLU D:83 , HIS D:98
BINDING SITE FOR RESIDUE NI D 251
09
AC8
SOFTWARE
MET D:10 , ASP D:102 , GLU D:105 , HIS D:106 , HOH D:253
BINDING SITE FOR RESIDUE NI D 252
10
AP
UNKNOWN
NI A:252 , MET A:10 , ASP A:102 , GLU A:105 , HIS A:106 , HOH A:253
NULL
11
BA
UNKNOWN
NI B:251 , HIS B:79 , GLU B:83 , HIS B:98
NULL
12
BP
UNKNOWN
NI B:252 , MET B:10 , ASP B:102 , GLU B:105 , HIS B:106 , HOH B:253
NULL
13
CA
UNKNOWN
NI C:251 , HIS C:79 , GLU C:83 , HIS C:98
NULL
14
CP
UNKNOWN
NI C:252 , MET C:10 , ASP C:102 , GLU C:105 , HIS C:106 , HOH C:253
NULL
15
DA
UNKNOWN
NI D:251 , HIS D:79 , GLU D:83 , HIS D:98
NULL
16
DP
UNKNOWN
NI D:252 , MET D:10 , ASP D:102 , GLU D:105 , HIS D:106 , HOH D:253
NULL
[
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]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_DTXR_CORDI_001 (R47H, chain A/B/C/D, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_DTXR_CORDI_001
*
R
47
H
DTXR_CORDI
---
---
A/B/C/D
R
47
H
* 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,B:4-65,C:4-65,D:4-65,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
4
A:4-65
B:4-65
C:4-65
D:4-65
DTXR_CORDW
4-65
4
A:4-65
B:4-65
C:4-65
D:4-65
[
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Exons
(0, 0)
Info
All Exons
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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.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1ddna1 (A:3-64)
1b: SCOP_d1ddnb1 (B:3-64)
1c: SCOP_d1ddnc1 (C:3-64)
1d: SCOP_d1ddnd1 (D:3-64)
2a: SCOP_d1ddna2 (A:65-120)
2b: SCOP_d1ddnb2 (B:65-120)
2c: SCOP_d1ddnc2 (C:65-120)
2d: SCOP_d1ddnd2 (D:65-120)
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Classes
(
)
(
)
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(
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
d1ddna1
A:3-64
1b
d1ddnb1
B:3-64
1c
d1ddnc1
C:3-64
1d
d1ddnd1
D: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
d1ddna2
A:65-120
2b
d1ddnb2
B:65-120
2c
d1ddnc2
C:65-120
2d
d1ddnd2
D:65-120
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1ddnA01 (A:3-75)
1b: CATH_1ddnB01 (B:3-75)
1c: CATH_1ddnC01 (C:3-75)
1d: CATH_1ddnD01 (D:3-75)
2a: CATH_1ddnA02 (A:76-120)
2b: CATH_1ddnB02 (B:76-120)
2c: CATH_1ddnC02 (C:76-120)
2d: CATH_1ddnD02 (D:76-120)
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
'winged helix' repressor DNA binding domain
(507)
[unclassified]
(77)
1a
1ddnA01
A:3-75
1b
1ddnB01
B:3-75
1c
1ddnC01
C:3-75
1d
1ddnD01
D:3-75
Topology
:
Diphtheria Toxin Repressor; domain 2
(34)
Homologous Superfamily
:
Diphtheria Toxin Repressor, domain 2
(32)
[unclassified]
(5)
2a
1ddnA02
A:76-120
2b
1ddnB02
B:76-120
2c
1ddnC02
C:76-120
2d
1ddnD02
D:76-120
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Protein & NOT PROSITE
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Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
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