9YD2 image
Deposition Date 2025-09-20
Release Date 2026-06-24
Last Version Date 2026-06-24
Entry Detail
PDB ID:
9YD2
Keywords:
REPLICATION
Title:
Ternary complex of DNA polymerase I from Bacillus stearothermophilus, large fragment, bound to DNA containing a thymine dimer and dATP
Biological Source:
Source Organism(s):
Geobacillus stearothermophilus (Taxon ID: 1422)
synthetic construct (Taxon ID: 32630)
Expression System(s):
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.25 Å
R-Value Free:
0.28
R-Value Work:
0.22
Space Group:
P 31 2 1
9YD2 validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA polymerase I
Gene (Uniprot):DPO1
Mutagens:D598A
Chain IDs:A
Chain Length:581
Number of Molecules:1
Biological Source:Geobacillus stearothermophilus
UniProt ID:D9N168 EC:2.7.7.7
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*AP*AP*GP*GP*AP*
Chain IDs:B
Chain Length:11
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*(TTD)P*CP*AP*CP
Chain IDs:C
Chain Length:15
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
DTP
MN
SO4
Primary Citation
Structural basis for blockage of DNA synthesis by a thymine dimer lesion in a high-fidelity DNA polymerase
Biochemistry ? ? ? (2026)
DOI: 10.1021/acs.biochem.5c00781
Primary Citation of related structures
9YD2
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