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1TKD
Biol. Unit 1
Info
Asym.Unit (168 KB)
Biol.Unit 1 (161 KB)
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(1)
Title
:
T7 DNA POLYMERASE TERNARY COMPLEX WITH 8 OXO GUANOSINE AND DCMP AT THE ELONGATION SITE
Authors
:
L. G. Brieba, B. F. Eichman, R. J. Kokoska, S. Doublie, T. A. Kunkel, T. Ellenberger
Date
:
08 Jun 04 (Deposition) - 31 Aug 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.49
Chains
:
Asym. Unit : A,B,P,T
Biol. Unit 1: A,B,P,T (1x)
Keywords
:
8-Oxoguanosine Dna Polymerase, Transferase/Electron Transport/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. G. Brieba, B. F. Eichman, R. J. Kokoska, S. Doublie, T. A. Kunkel, T. Ellenberger
Structural Basis For The Dual Coding Potential Of 8-Oxoguanosine By A High-Fidelity Dna Polymerase.
Embo J. V. 23 3452 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(6, 8)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
2a: 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPH... (8OGa)
3a: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOS... (D3Ta)
4a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
5a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
6c: MAGNESIUM ION (MGc)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
1
Ligand/Ion
PENTAETHYLENE GLYCOL
2
8OG
1
Mod. Nucleotide
8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
3
D3T
1
Ligand/Ion
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
4
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
5
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
6
MG
-1
Ligand/Ion
MAGNESIUM ION
7
SO4
3
Ligand/Ion
SULFATE ION
[
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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:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:475 , ALA A:476 , ASP A:654 , D3T A:823 , MG A:902
BINDING SITE FOR RESIDUE MG A 901
2
AC2
SOFTWARE
ASP A:475 , ASP A:654 , D3T A:823 , MG A:901 , HOH A:1372 , HOH A:1507
BINDING SITE FOR RESIDUE MG A 902
3
AC3
SOFTWARE
ASP A:5 , HOH A:1091 , HOH A:1093 , HOH A:1094 , HOH A:1479 , HOH A:1480
BINDING SITE FOR RESIDUE MG A 903
4
AC4
SOFTWARE
LYS A:226 , ARG A:229 , HOH A:1022 , HOH A:1088 , HOH A:1277 , HOH A:1609
BINDING SITE FOR RESIDUE SO4 A 904
5
AC5
SOFTWARE
LYS A:184 , ARG A:661 , HOH A:1075 , HOH A:1415
BINDING SITE FOR RESIDUE SO4 A 905
6
AC6
SOFTWARE
ASN A:162 , ARG A:255 , LYS A:256 , THR A:279 , LYS A:281 , HOH A:1393
BINDING SITE FOR RESIDUE SO4 A 906
7
AC7
SOFTWARE
ARG A:429 , ASP A:475 , ALA A:476 , GLY A:478 , LEU A:479 , GLU A:480 , HIS A:506 , ARG A:518 , LYS A:522 , TYR A:526 , ASP A:654 , MG A:901 , MG A:902 , HOH A:1178 , HOH A:1205 , HOH A:1608 , DOC P:822 , DA T:854 , 8OG T:855
BINDING SITE FOR RESIDUE D3T A 823
8
AC8
SOFTWARE
LEU A:77 , ASN A:78 , ARG A:79 , HOH A:1188 , HOH A:1341 , ILE B:5 , HIS B:6 , SER B:11 , THR B:14 , ASP B:15
BINDING SITE FOR RESIDUE MES A 991
9
AC9
SOFTWARE
ALA A:10 , TYR A:64 , MET A:107 , LEU A:109 , LYS A:136 , TRP A:160 , HOH A:1405
BINDING SITE FOR RESIDUE 1PE A 992
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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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)
;
View:
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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)
Info
All Exons
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All Exon Boundaries
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Note:
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, 3)
Info
All SCOP Domains
1a: SCOP_d1tkda1 (A:1-210)
2a: SCOP_d1tkdb_ (B:)
3a: SCOP_d1tkda2 (A:211-704)
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Classes
(
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(
)
Families
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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
d1tkda1
A:1-210
Fold
:
Thioredoxin fold
(994)
Superfamily
:
Thioredoxin-like
(992)
Family
:
Thioltransferase
(167)
Protein domain
:
Thioredoxin
(106)
Escherichia coli [TaxId: 562]
(47)
2a
d1tkdb_
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
d1tkda2
A:211-704
[
close SCOP info
]
CATH Domains
(5, 5)
Info
all CATH domains
1a: CATH_1tkdA03 (A:415-477,A:590-704)
2a: CATH_1tkdA01 (A:1-232)
3a: CATH_1tkdB00 (B:3-107)
4a: CATH_1tkdA04 (A:478-589)
5a: CATH_1tkdA02 (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
1tkdA03
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
1tkdA01
A:1-232
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Glutaredoxin
(620)
Homologous Superfamily
:
Glutaredoxin
(617)
[unclassified]
(18)
3a
1tkdB00
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
1tkdA04
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
1tkdA02
A:233-414
[
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]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_RNase_H_2_1tkdA01 (A:2-186)
2a: PFAM_Thioredoxin_1tkdB01 (B:3-106)
3a: PFAM_DNA_pol_A_1tkdA02 (A:308-703)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
RNase_H
(288)
Family
:
RNase_H_2
(16)
Enterobacteria phage T7 (Bacteriophage T7)
(16)
1a
RNase_H_2-1tkdA01
A:2-186
Clan
:
Thioredoxin
(367)
Family
:
Thioredoxin
(82)
Escherichia coli (strain K12)
(25)
2a
Thioredoxin-1tkdB01
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-1tkdA02
A:308-703
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]
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Sidechain
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Protein & NOT Site
Protein & NOT PROSITE
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Chain P
Chain T
Asymmetric Unit 1
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