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Asym. Unit
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Asym.Unit (126 KB)
Biol.Unit 1 (118 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A TWO-DOMAIN IDER-DNA COMPLEX CRYSTAL FORM II
Authors
:
G. Wisedchaisri, C. J. Chou, M. Wu, C. Roach, A. E. Rice, R. K. Holmes, C. Beeson, W. G. Hol
Date
:
18 Oct 06 (Deposition) - 13 Feb 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Dna-Binding Protein, Transcription/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Wisedchaisri, C. J. Chou, M. Wu, C. Roach, A. E. Rice, R. K. Holmes, C. Beeson, W. G. Hol
Crystal Structures, Metal Activation, And Dna-Binding Properties Of Two-Domain Ider From Mycobacterium Tuberculosis
Biochemistry V. 46 436 2007
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 22)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
1i: ACETATE ION (ACTi)
1j: ACETATE ION (ACTj)
2a: NICKEL (II) ION (NIa)
2b: NICKEL (II) ION (NIb)
2c: NICKEL (II) ION (NIc)
2d: NICKEL (II) ION (NId)
2e: NICKEL (II) ION (NIe)
2f: NICKEL (II) ION (NIf)
2g: NICKEL (II) ION (NIg)
2h: NICKEL (II) ION (NIh)
2i: NICKEL (II) ION (NIi)
2j: NICKEL (II) ION (NIj)
2k: NICKEL (II) ION (NIk)
2l: NICKEL (II) ION (NIl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
10
Ligand/Ion
ACETATE ION
2
NI
12
Ligand/Ion
NICKEL (II) ION
[
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]
Sites
(22, 22)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:79 , GLU A:83 , HIS A:98 , ACT A:2001
BINDING SITE FOR RESIDUE NI A 1001
02
AC2
SOFTWARE
MET A:10 , CYS A:102 , GLU A:105 , HIS A:106
BINDING SITE FOR RESIDUE NI A 1002
03
AC3
SOFTWARE
HIS A:61 , GLU A:63 , ACT A:2002 , ACT A:2003
BINDING SITE FOR RESIDUE NI A 1003
04
AC4
SOFTWARE
HIS B:79 , GLU B:83 , HIS B:98 , ACT B:2001
BINDING SITE FOR RESIDUE NI B 1001
05
AC5
SOFTWARE
MET B:10 , CYS B:102 , GLU B:105 , HIS B:106
BINDING SITE FOR RESIDUE NI B 1002
06
AC6
SOFTWARE
ASP B:59 , HIS B:61 , GLU B:63 , ACT B:2002
BINDING SITE FOR RESIDUE NI B 1003
07
AC7
SOFTWARE
HIS C:79 , GLU C:83 , HIS C:98 , ACT C:2001
BINDING SITE FOR RESIDUE NI C 1001
08
AC8
SOFTWARE
MET C:10 , CYS C:102 , GLU C:105 , HIS C:106 , HOH C:2007
BINDING SITE FOR RESIDUE NI C 1002
09
AC9
SOFTWARE
ASP C:59 , HIS C:61 , GLU C:63 , ACT C:2002 , ACT C:2003
BINDING SITE FOR RESIDUE NI C 1003
10
BC1
SOFTWARE
HIS D:79 , GLU D:83 , HIS D:98 , ACT D:2001
BINDING SITE FOR RESIDUE NI D 1001
11
BC2
SOFTWARE
MET D:10 , ARG D:13 , CYS D:102 , GLU D:105 , HIS D:106
BINDING SITE FOR RESIDUE NI D 1002
12
BC3
SOFTWARE
ASP D:59 , HIS D:61 , GLU D:63 , ACT D:2002
BINDING SITE FOR RESIDUE NI D 1003
13
BC4
SOFTWARE
HIS A:79 , GLU A:83 , HIS A:98 , ASN A:130 , NI A:1001
BINDING SITE FOR RESIDUE ACT A 2001
14
BC5
SOFTWARE
HIS A:61 , GLU A:63 , NI A:1003
BINDING SITE FOR RESIDUE ACT A 2002
15
BC6
SOFTWARE
ASP A:59 , HIS A:61 , GLU A:63 , NI A:1003
BINDING SITE FOR RESIDUE ACT A 2003
16
BC7
SOFTWARE
HIS B:79 , GLU B:83 , HIS B:98 , ASN B:130 , NI B:1001
BINDING SITE FOR RESIDUE ACT B 2001
17
BC8
SOFTWARE
HIS B:61 , GLU B:63 , NI B:1003
BINDING SITE FOR RESIDUE ACT B 2002
18
BC9
SOFTWARE
HIS C:79 , ARG C:80 , GLU C:83 , HIS C:98 , ASN C:130 , NI C:1001
BINDING SITE FOR RESIDUE ACT C 2001
19
CC1
SOFTWARE
ASP A:88 , HIS C:61 , GLU C:63 , NI C:1003
BINDING SITE FOR RESIDUE ACT C 2002
20
CC2
SOFTWARE
ASP C:59 , GLU C:63 , NI C:1003
BINDING SITE FOR RESIDUE ACT C 2003
21
CC3
SOFTWARE
HIS D:79 , GLU D:83 , HIS D:98 , NI D:1001
BINDING SITE FOR RESIDUE ACT D 2001
22
CC4
SOFTWARE
ASP D:59 , HIS D:61 , GLU D:63 , NI D:1003
BINDING SITE FOR RESIDUE ACT D 2002
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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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.
IDER_MYCTO
4-65
4
A:4-65
B:4-65
C:4-65
D:4-65
IDER_MYCTU
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_d2it0a1 (A:3-64)
1b: SCOP_d2it0b1 (B:3-64)
1c: SCOP_d2it0c1 (C:3-64)
1d: SCOP_d2it0d1 (D:3-64)
2a: SCOP_d2it0a2 (A:65-147)
2b: SCOP_d2it0b2 (B:65-147)
2c: SCOP_d2it0c2 (C:65-139)
2d: SCOP_d2it0d2 (D:65-139)
View:
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Classes
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)
(
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Folds
(
)
(
)
Superfamilies
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)
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)
Families
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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
:
Iron-dependent regulator IdeR
(6)
Mycobacterium tuberculosis [TaxId: 1773]
(6)
1a
d2it0a1
A:3-64
1b
d2it0b1
B:3-64
1c
d2it0c1
C:3-64
1d
d2it0d1
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
:
Iron-dependent regulator
(6)
Mycobacterium tuberculosis [TaxId: 1773]
(6)
2a
d2it0a2
A:65-147
2b
d2it0b2
B:65-147
2c
d2it0c2
C:65-139
2d
d2it0d2
D:65-139
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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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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Sidechain
Hetero
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
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Asym.Unit (126 KB)
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