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3RRH
Asym. Unit
Info
Asym.Unit (213 KB)
Biol.Unit 1 (205 KB)
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(1)
Title
:
TERNARY STRUCTURE OF THE LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO AN ABASIC SITE AND A DDTTP
Authors
:
A. Marx, K. Diederichs, S. Obeid
Date
:
29 Apr 11 (Deposition) - 15 Feb 12 (Release) - 09 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Dna Polymerase, Abasic Site, Translesion Synthesis, A-Rule, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Obeid, W. Welte, K. Diederichs, A. Marx
Amino Acid Templating Mechanisms In Selection Of Nucleotide Opposite Abasic Sites By A Family A Dna Polymerase.
J. Biol. Chem. V. 287 14099 2012
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Hetero Components
(7, 12)
Info
All Hetero Components
1a: 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE (2DTa)
2a: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRa)
3a: ACETATE ION (ACTa)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
6a: TRIETHYLENE GLYCOL (PGEa)
6b: TRIETHYLENE GLYCOL (PGEb)
7a: THYMIDINE-5'-TRIPHOSPHATE (TTPa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
2DT
1
Mod. Nucleotide
3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2
3DR
1
Mod. Nucleotide
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
3
ACT
1
Ligand/Ion
ACETATE ION
4
GOL
4
Ligand/Ion
GLYCEROL
5
MG
2
Ligand/Ion
MAGNESIUM ION
6
PGE
2
Ligand/Ion
TRIETHYLENE GLYCOL
7
TTP
1
Ligand/Ion
THYMIDINE-5'-TRIPHOSPHATE
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:67 , HOH A:85 , HOH A:171 , GLN A:613 , HIS A:639 , ARG A:659 , LYS A:663 , PHE A:667 , TYR A:671 , ASP A:785 , MG A:833 , HOH A:854 , HOH A:875 , HOH A:876 , HOH A:888 , 2DT B:112
BINDING SITE FOR RESIDUE TTP A 1
02
AC2
SOFTWARE
TTP A:1 , HOH A:875 , HOH A:876
BINDING SITE FOR RESIDUE MG A 833
03
AC3
SOFTWARE
HOH A:149 , THR A:544 , TYR A:545 , PRO A:579 , ASN A:580 , ASN A:583 , DC C:209 , DC C:210
BINDING SITE FOR RESIDUE GOL A 834
04
AC4
SOFTWARE
ARG A:313
BINDING SITE FOR RESIDUE PGE A 835
05
AC5
SOFTWARE
HOH A:74 , HOH A:276 , ARG A:425 , TRP A:428
BINDING SITE FOR RESIDUE GOL A 836
06
AC6
SOFTWARE
SER A:644 , HOH A:893
BINDING SITE FOR RESIDUE ACT A 837
07
AC7
SOFTWARE
HOH B:20 , HOH B:43 , HOH B:176 , HOH C:144 , HOH C:290
BINDING SITE FOR RESIDUE MG B 1
08
AC8
SOFTWARE
HOH A:90 , HOH B:43 , HOH B:63 , DC B:106 , DG B:107
BINDING SITE FOR RESIDUE PGE B 113
09
AC9
SOFTWARE
DG C:213 , DG C:214 , DT C:215 , HOH C:365
BINDING SITE FOR RESIDUE GOL C 1
10
BC1
SOFTWARE
ALA A:570 , ARG A:728 , DG C:206 , DC C:207 , HOH C:287
BINDING SITE FOR RESIDUE GOL C 217
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_A (A:659-678)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_A
PS00447
DNA polymerase family A signature.
DPO1_THEAQ
659-678
1
A:659-678
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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.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3rrha1 (A:295-422)
2a: SCOP_d3rrha2 (A:423-832)
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Classes
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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 prokaryotic DNA polymerase
(81)
Thermus aquaticus [TaxId: 271]
(24)
1a
d3rrha1
A:295-422
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
:
DNA polymerase I (Klenow fragment)
(82)
Thermus aquaticus [TaxId: 271]
(24)
2a
d3rrha2
A:423-832
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (213 KB)
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