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2AJQ
Biol. Unit 2
Info
Asym.Unit (305 KB)
Biol.Unit 1 (152 KB)
Biol.Unit 2 (151 KB)
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(1)
Title
:
STRUCTURE OF REPLICATIVE DNA POLYMERASE PROVIDES INSIGTS INTO THE MECHANISMS FOR PROCESSIVITY, FRAMESHIFTING AND EDITING
Authors
:
L. Brieba, T. Ellenberger
Date
:
02 Aug 05 (Deposition) - 26 Sep 06 (Release) - 17 Nov 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,F,I,P,T,X,Z
Biol. Unit 1: A,B,P,T (1x)
Biol. Unit 2: F,I,X,Z (1x)
Keywords
:
Polymerase T7; X-Ray Crystallography; Ternary Complex, Transferase, Transcription/Dna Complex, Transferase, Transcription/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Brieba, T. Ellenberger
Structure Of Replicative Dna Polymerase Provides Insigts Into The Mechanisms For Processivity, Frameshifting And Editing
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE (2DTa)
1b: 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE (2DTb)
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No.
Name
Count
Type
Full Name
1
2DT
1
Mod. Nucleotide
3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
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Sites
(0, 0)
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SAPs(SNPs)/Variants
(0, 0)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: THIOREDOXIN_1 (I:24-42)
2: DNA_POLYMERASE_A (F:518-537)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THIOREDOXIN_1
PS00194
Thioredoxin family active site.
THIO_ECOLI
25-43
1
-
I:24-42
2
DNA_POLYMERASE_A
PS00447
DNA polymerase family A signature.
DPOL_BPT7
518-537
1
-
F:518-537
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2ajqa1 (A:1-210)
1b: SCOP_d2ajqf1 (F:1-210)
2a: SCOP_d2ajqb_ (B:)
2b: SCOP_d2ajqi_ (I:)
3a: SCOP_d2ajqa2 (A:211-704)
3b: SCOP_d2ajqf2 (F:211-704)
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(
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)
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)
(
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)
(
)
Protein Domains
(
)
(
)
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
d2ajqa1
A:1-210
1b
d2ajqf1
F:1-210
Fold
:
Thioredoxin fold
(994)
Superfamily
:
Thioredoxin-like
(992)
Family
:
Thioltransferase
(167)
Protein domain
:
Thioredoxin
(106)
Escherichia coli [TaxId: 562]
(47)
2a
d2ajqb_
B:
2b
d2ajqi_
I:
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
d2ajqa2
A:211-704
3b
d2ajqf2
F:211-704
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CATH Domains
(5, 10)
Info
all CATH domains
1a: CATH_2ajqA03 (A:415-477,A:590-704)
1b: CATH_2ajqF03 (F:415-477,F:590-704)
2a: CATH_2ajqA01 (A:1-232)
2b: CATH_2ajqF01 (F:1-232)
3a: CATH_2ajqB00 (B:3-107)
3b: CATH_2ajqI00 (I:3-107)
4a: CATH_2ajqA04 (A:478-589)
4b: CATH_2ajqF04 (F:478-589)
5a: CATH_2ajqF02 (F:233-414)
5b: CATH_2ajqA02 (A:233-414)
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)
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(
)
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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
2ajqA03
A:415-477,A:590-704
1b
2ajqF03
F:415-477,F:590-704
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
[unclassified]
(102)
2a
2ajqA01
A:1-232
2b
2ajqF01
F:1-232
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Glutaredoxin
(620)
Homologous Superfamily
:
Glutaredoxin
(617)
[unclassified]
(18)
3a
2ajqB00
B:3-107
3b
2ajqI00
I: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
2ajqA04
A:478-589
4b
2ajqF04
F: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
2ajqF02
F:233-414
5b
2ajqA02
A:233-414
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (305 KB)
Header - Asym.Unit
Biol.Unit 1 (152 KB)
Header - Biol.Unit 1
Biol.Unit 2 (151 KB)
Header - Biol.Unit 2
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