Structure of PDB 8ppv Chain A Binding Site BS01

Receptor Information

>8ppv Chain A (length=447) Species: 272844 (Pyrococcus abyssi GE5)

EYSKYEDVVIEWNPSVTPVQIEKNYEVKFDVRQVKLRPPKVKNGSGKEGE
IIVEAYASLFKSRLSKLKRILRENPEISNVVDIGKLNYVSGDEEVTIIGL
VNSKRETNRGLIFEVEDKTGIVKVFLPKDSEDYREAFKVLPDAVVAFKGF
YSKKGIFFANKFYLPDVPLYRKQKPPLEEKVYAILISDIHVGSREFCEKA
FLKFLEWLNGHVESKEEEEIVSRVKYLIIAGDVVDGIGIYPGQYSDLVIP
DIFDQYEALANLLANVPEHITMFIGPGNADAARPAIPQPEFYKEYAKPIY
KLKNAIIISNPAVIRLHGRDFLIAHGRGIEDVVSFVPGLTHHKPGLPMVE
LLKMRHLAPTFGGKVPIAPDPEDLLVIEEVPDLVQMGHVHVYDAVVYRGV
QLVNSATWQAQTEFQKMVNIVPTPAKVPVVDVESARVVKVLDFSGWC

Ligand information

>8ppv Chain P (length=19)

ccgggccgagccgtgcuuu

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ppv Molecular basis for proof-reading by Family-D DNA polymerases
• Resolution: 3.02 Å
• Binding residue (original residue number in PDB): Y412 P413 F586
• Binding residue (residue number reindexed from 1): Y240 P241 F414

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  3.1.11.1: exodeoxyribonuclease I.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0004527 exonuclease activity
• GO:0008310 single-stranded DNA 3'-5' DNA exonuclease activity
• GO:0008408 3'-5' exonuclease activity

Biological Process

• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006271 DNA strand elongation involved in DNA replication
• GO:0006308 DNA catabolic process
• GO:0071897 DNA biosynthetic process

Cellular Component

• GO:0042575 DNA polymerase complex

External links

• PDB: RCSB:8ppv, PDBe:8ppv, PDBj:8ppv
• PDBsum: 8ppv
• PubMed: 38097591
• UniProt: Q9V2F3|DP2S_PYRAB DNA polymerase II small subunit (Gene Name=polB)