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1ZRF
Asym. Unit
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Asym.Unit (108 KB)
Biol.Unit 1 (103 KB)
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(1)
Title
:
4 CRYSTAL STRUCTURES OF CAP-DNA WITH ALL BASE-PAIR SUBSTITUTIONS AT POSITION 6, CAP-[6C;17G]ICAP38 DNA
Authors
:
H. M. Berman, A. A. Napoli
Date
:
19 May 05 (Deposition) - 21 Mar 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,W,X,Y,Z
Biol. Unit 1: A,B,W,X,Y,Z (1x)
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
:
A. A. Napoli, C. L. Lawson, R. H. Ebright, H. M. Berman
Indirect Readout Of Dna Sequence At The Primary-Kink Site In The Cap-Dna Complex: Recognition Of Pyrimidine-Purine And Purine-Purine Steps.
J. Mol. Biol. V. 357 173 2006
(for further references see the
PDB file header
)
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Hetero Components
(2, 9)
Info
All Hetero Components
1a: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHA... (CMPa)
1b: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHA... (CMPb)
1c: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHA... (CMPc)
1d: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHA... (CMPd)
2a: 1,4-DIETHYLENE DIOXIDE (DIOa)
2b: 1,4-DIETHYLENE DIOXIDE (DIOb)
2c: 1,4-DIETHYLENE DIOXIDE (DIOc)
2d: 1,4-DIETHYLENE DIOXIDE (DIOd)
2e: 1,4-DIETHYLENE DIOXIDE (DIOe)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CMP
4
Ligand/Ion
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2
DIO
5
Ligand/Ion
1,4-DIETHYLENE DIOXIDE
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:49 , GLY A:71 , GLU A:72 , LEU A:73 , ARG A:82 , SER A:83 , ALA A:84 , THR A:127 , HOH A:2625 , HOH A:2626 , HOH A:2656 , LEU B:124 , SER B:128
BINDING SITE FOR RESIDUE CMP A 622
2
AC2
SOFTWARE
SER A:128 , VAL B:49 , ILE B:70 , GLY B:71 , GLU B:72 , LEU B:73 , ARG B:82 , SER B:83 , ALA B:84 , THR B:127 , HOH B:3628 , HOH B:3639
BINDING SITE FOR RESIDUE CMP B 1622
3
AC3
SOFTWARE
LYS A:57 , GLU A:58 , GLN A:170 , GLY A:173 , GLN A:174 , GLY A:177 , CYS A:178 , ARG A:180 , HOH A:2639 , ALA B:135
BINDING SITE FOR RESIDUE CMP A 2622
4
AC4
SOFTWARE
ALA A:135 , LYS B:57 , GLU B:58 , GLN B:170 , GLY B:173 , GLN B:174 , GLY B:177 , CYS B:178 , SER B:179 , ARG B:180 , HOH B:3690 , DA Z:9
BINDING SITE FOR RESIDUE CMP B 3622
5
AC5
SOFTWARE
ALA B:144
BINDING SITE FOR RESIDUE DIO B 301
6
AC6
SOFTWARE
LYS B:130 , ARG B:142 , THR B:146 , ILE B:175 , VAL B:176
BINDING SITE FOR RESIDUE DIO B 302
7
AC7
SOFTWARE
LEU A:148 , LEU A:195 , VAL A:205
BINDING SITE FOR RESIDUE DIO A 303
8
AC8
SOFTWARE
LEU A:11 , PHE A:14 , TYR A:41 , PHE A:69 , ILE A:112 , ARG A:115 , ARG A:209
BINDING SITE FOR RESIDUE DIO A 304
9
AC9
SOFTWARE
LYS A:130 , ARG A:142 , THR A:146 , ILE A:175 , VAL A:176 , HOH A:2661
BINDING SITE FOR RESIDUE DIO A 305
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(5, 10)
Info
All PROSITE Patterns/Profiles
1: CNMP_BINDING_3 (A:23-123,B:23-123)
2: CNMP_BINDING_1 (A:29-45,B:29-45)
3: CNMP_BINDING_2 (A:70-88,B:70-88)
4: HTH_CRP_2 (A:137-209,B:137-207)
5: HTH_CRP_1 (A:167-190,B:167-190)
;
View:
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End label:
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
2
A:23-123
B:23-123
2
CNMP_BINDING_1
PS00888
Cyclic nucleotide-binding domain signature 1.
CRP_ECOLI
30-46
2
A:29-45
B:29-45
3
CNMP_BINDING_2
PS00889
Cyclic nucleotide-binding domain signature 2.
CRP_ECOLI
71-89
2
A:70-88
B:70-88
4
HTH_CRP_2
PS51063
Crp-type HTH domain profile.
CRP_ECOLI
138-210
2
A:137-209
B:137-207
5
HTH_CRP_1
PS00042
Crp-type HTH domain signature.
CRP_ECOLI
168-191
2
A:167-190
B:167-190
[
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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.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1zrfa1 (A:138-209)
1b: SCOP_d1zrfb1 (B:138-207)
2a: SCOP_d1zrfa2 (A:7-137)
2b: SCOP_d1zrfb2 (B:8-137)
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Protein Domains
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(
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Organisms
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(
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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
:
CAP C-terminal domain-like
(39)
Protein domain
:
Catabolite gene activator protein (CAP), C-terminal domain
(24)
Escherichia coli [TaxId: 562]
(24)
1a
d1zrfa1
A:138-209
1b
d1zrfb1
B: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
d1zrfa2
A:7-137
2b
d1zrfb2
B:8-137
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1zrfA02 (A:138-209)
1b: CATH_1zrfB02 (B:138-207)
2a: CATH_1zrfA01 (A:7-137)
2b: CATH_1zrfB01 (B:8-137)
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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
1zrfA02
A:138-209
1b
1zrfB02
B:138-207
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Jelly Rolls
(177)
[unclassified]
(14)
2a
1zrfA01
A:7-137
2b
1zrfB01
B:8-137
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Pfam Domains
(0, 0)
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