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1O3Q
Asym. Unit
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Asym.Unit (49 KB)
Biol.Unit 1 (88 KB)
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(1)
Title
:
PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES
Authors
:
S. Chen, J. Vojtechovsky, G. N. Parkinson, R. H. Ebright, H. M. Berman
Date
:
18 Mar 03 (Deposition) - 08 Apr 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Keywords
:
Protein-Dna Complex, Cap, Cap-Dna, Catabolite Gene Activator Protein, Camp Receptor Protein, Crp, Gene Regulation/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Chen, J. Vojtechovsky, G. N. Parkinson, R. H. Ebright, H. M. Berman
Indirect Readout Of Dna Sequence At The Primary-Kink Site In The Cap-Dna Complex: Dna Binding Specificity Based On Energetics Of Dna Kinking
J. Mol. Biol. V. 314 63 2001
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHA... (CMPa)
1b: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHA... (CMPb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CMP
2
Ligand/Ion
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:49 , ILE A:70 , GLY A:71 , GLU A:72 , LEU A:73 , ARG A:82 , SER A:83 , ALA A:84 , LEU A:124 , THR A:127 , SER A:128
BINDING SITE FOR RESIDUE CMP A 1
2
AC2
SOFTWARE
LYS A:57 , GLU A:58 , MET A:59 , ALA A:135 , GLN A:170 , GLY A:173 , GLN A:174 , CYS A:178 , ARG A:180 , DA C:9
BINDING SITE FOR RESIDUE CMP A 2
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(5, 5)
Info
All PROSITE Patterns/Profiles
1: CNMP_BINDING_3 (A:23-123)
2: CNMP_BINDING_1 (A:29-45)
3: CNMP_BINDING_2 (A:70-88)
4: HTH_CRP_2 (A:137-207)
5: HTH_CRP_1 (A:167-190)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CNMP_BINDING_3
PS50042
cAMP/cGMP binding motif profile.
CRP_ECOLI
24-124
1
A:23-123
2
CNMP_BINDING_1
PS00888
Cyclic nucleotide-binding domain signature 1.
CRP_ECOLI
30-46
1
A:29-45
3
CNMP_BINDING_2
PS00889
Cyclic nucleotide-binding domain signature 2.
CRP_ECOLI
71-89
1
A:70-88
4
HTH_CRP_2
PS51063
Crp-type HTH domain profile.
CRP_ECOLI
138-210
1
A:137-207
5
HTH_CRP_1
PS00042
Crp-type HTH domain signature.
CRP_ECOLI
168-191
1
A:167-190
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1o3qa1 (A:138-207)
2a: SCOP_d1o3qa2 (A:8-137)
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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
:
CAP C-terminal domain-like
(39)
Protein domain
:
Catabolite gene activator protein (CAP), C-terminal domain
(24)
Escherichia coli [TaxId: 562]
(24)
1a
d1o3qa1
A:138-207
Class
:
All beta proteins
(24004)
Fold
:
Double-stranded beta-helix
(580)
Superfamily
:
cAMP-binding domain-like
(99)
Family
:
cAMP-binding domain
(78)
Protein domain
:
Catabolite gene activator protein, N-terminal domain
(28)
Escherichia coli [TaxId: 562]
(28)
2a
d1o3qa2
A:8-137
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1o3qA02 (A:138-206)
2a: CATH_1o3qA01 (A:9-137)
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)
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)
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)
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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
1o3qA02
A:138-206
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Jelly Rolls
(177)
[unclassified]
(14)
2a
1o3qA01
A:9-137
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Crp_1o3qA01 (A:165-196)
2a: PFAM_cNMP_binding_1o3qA02 (A:20-111)
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Clans
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(
)
Organisms
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)
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)
Clan
:
HTH
(544)
Family
:
Crp
(12)
Escherichia coli (strain K12)
(10)
1a
Crp-1o3qA01
A:165-196
Clan
:
no clan defined [family: cNMP_binding]
(41)
Family
:
cNMP_binding
(41)
Escherichia coli (strain K12)
(10)
2a
cNMP_binding-1o3qA02
A:20-111
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Asymmetric Unit 1
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