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Asym. Unit
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Asym.Unit (139 KB)
Biol.Unit 1 (133 KB)
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Title
:
T7 DNA POLYMERASE IN COMPLEX WITH A PRIMER/TEMPLATE DNA CONTAINING A DISORDERED N-2 AMINOFLUORENE ON THE TEMPLATE, CRYSTALLIZED WITH DIDEOXY-ATP AS THE INCOMING NUCLEOTIDE.
Authors
:
S. Dutta, Y. Li, D. Johnson, L. Dzantiev, C. C. Richardson, L. J. Romano, T. Ellenberger
Date
:
24 Aug 04 (Deposition) - 26 Oct 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Dna Polymerase, N-2-Aminofluorene, Mutagenesis, Replication Block, Transferase/Electron Transport/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Dutta, Y. Li, D. Johnson, L. Dzantiev, C. C. Richardson, L. J. Romano, T. Ellenberger
Crystal Structures Of 2-Acetylaminofluorene And 2-Aminofluorene In Complex With T7 Dna Polymerase Reveal Mechanisms Of Mutagenesis.
Proc. Natl. Acad. Sci. Usa V. 101 16186 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE (2DTa)
2a: MAGNESIUM ION (MGa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
2DT
1
Mod. Nucleotide
3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2
MG
1
Ligand/Ion
MAGNESIUM ION
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:5 , HIS A:59 , ASP A:65 , HOH A:4013
BINDING SITE FOR RESIDUE MG A 3001
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: THIOREDOXIN_1 (B:24-42)
2: DNA_POLYMERASE_A (A:518-537)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THIOREDOXIN_1
PS00194
Thioredoxin family active site.
THIO_ECOLI
25-43
1
B:24-42
2
DNA_POLYMERASE_A
PS00447
DNA polymerase family A signature.
DPOL_BPT7
518-537
1
A:518-537
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Exons
(0, 0)
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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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1x9wa1 (A:1-210)
2a: SCOP_d1x9wb_ (B:)
3a: SCOP_d1x9wa2 (A:211-704)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
DnaQ-like 3'-5' exonuclease
(253)
Protein domain
:
Exonuclease domain of T7 DNA polymerase
(17)
Bacteriophage T7 [TaxId: 10760]
(17)
1a
d1x9wa1
A:1-210
Fold
:
Thioredoxin fold
(994)
Superfamily
:
Thioredoxin-like
(992)
Family
:
Thioltransferase
(167)
Protein domain
:
Thioredoxin
(106)
Escherichia coli [TaxId: 562]
(47)
2a
d1x9wb_
B:
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
DNA polymerase I
(233)
Protein domain
:
T7 phage DNA polymerase
(17)
Bacteriophage T7 [TaxId: 10760]
(17)
3a
d1x9wa2
A:211-704
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CATH Domains
(5, 5)
Info
all CATH domains
1a: CATH_1x9wA03 (A:415-477,A:590-704)
2a: CATH_1x9wA01 (A:1-232)
3a: CATH_1x9wB00 (B:3-107)
4a: CATH_1x9wA04 (A:478-589)
5a: CATH_1x9wA02 (A:233-414)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.370, no name defined]
(99)
[unclassified]
(84)
1a
1x9wA03
A:415-477,A:590-704
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
[unclassified]
(102)
2a
1x9wA01
A:1-232
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Glutaredoxin
(620)
Homologous Superfamily
:
Glutaredoxin
(617)
[unclassified]
(18)
3a
1x9wB00
B:3-107
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
[unclassified]
(230)
4a
1x9wA04
A:478-589
Architecture
:
Up-down Bundle
(3216)
Topology
:
Taq DNA Polymerase; Chain T, domain 4
(88)
Homologous Superfamily
:
Taq DNA Polymerase; Chain T, domain 4
(88)
[unclassified]
(77)
5a
1x9wA02
A:233-414
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_RNase_H_2_1x9wA01 (A:2-186)
2a: PFAM_Thioredoxin_1x9wB01 (B:3-106)
3a: PFAM_DNA_pol_A_1x9wA02 (A:313-703)
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Clan
:
RNase_H
(288)
Family
:
RNase_H_2
(16)
Enterobacteria phage T7 (Bacteriophage T7)
(16)
1a
RNase_H_2-1x9wA01
A:2-186
Clan
:
Thioredoxin
(367)
Family
:
Thioredoxin
(82)
Escherichia coli (strain K12)
(25)
2a
Thioredoxin-1x9wB01
B:3-106
Clan
:
no clan defined [family: DNA_pol_A]
(69)
Family
:
DNA_pol_A
(69)
Enterobacteria phage T7 (Bacteriophage T7)
(16)
3a
DNA_pol_A-1x9wA02
A:313-703
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Asym.Unit (139 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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