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MolNFT v1 · #136715 · protein + DNA

DNA polymerase beta product complex with 8-OXOG:A and inserted dctp

5V1O · DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)…: “DNA polymerase beta product complex with 8-OXOG:A and inserted dctp”. X-ray diffraction, 4 ligands (PPV, NA, MG), 3 pockets (best druggability 0.70). MolNFT v1 #136715 on…

PDB
5V1O
Type
protein + DNA
Length
358 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
EC
2.7.7.7, 4.2.99.-
UniProt
P06746
Ligands
PPV, NA, MG, CL
Pockets
3 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
TDNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3')dna16——
PDNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG)P*C)-3')dna11——
DDNA (5'-D(P*GP*TP*CP*GP*G)-3')dna5——
ADNA polymerase beta (EC 2.7.7.7, 4.2.99.-)protein32651% helix, 13% strandP06746

Ligands and binding sites

  • PPV · Pyrophosphate · ligand · chains P, A
  • NA · Sodium ion · metal · 3 copies · chains P, A, D
  • MG · Magnesium ion · metal · 2 copies · chains P, A
  • CL · Chloride ion · ion · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
18870.700.7655MG, PPV
23370.620.7930empty
32100.570.8026empty

Interfaces

5 interfaces between chains.

  • T–A · 740 Ų buried · 17 hydrogen bonds · protein-nucleic
  • P–A · 544 Ų buried · 17 hydrogen bonds · protein-nucleic
  • T–P · 501 Ų buried · 44 hydrogen bonds · nucleic-nucleic
  • D–A · 372 Ų buried · 8 hydrogen bonds · protein-nucleic
  • T–D · 229 Ų buried · 19 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

  • 5V1O · DNA polymerase beta product complex with 8-oxoG:A and inserted dCTP · the same entry in another collection · chain T against T, TM-score 1.00
  • P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain A against A, TM-score 0.94

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