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MolNFT v1 · #137547 · protein + DNA

Human DNA polymerase beta 8-OXOG:DC extension with dttp after 20 S

5VRY · DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG)…: “Human DNA polymerase beta 8-OXOG:DC extension with dttp after 20 S”. X-ray diffraction, 4 ligands (TTP, PPV, MG), 3 pockets (best druggability 0.70). MolNFT v1 #137547 on GenesisL1: 3D…

PDB
5VRY
Type
protein + DNA
Length
359 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG) P*GP*CP*GP*CP*AP*TP*CP*AP*G)-3'); DNA…
EC
2.7.7.7, 4.2.99.-
UniProt
P06746
Ligands
TTP, PPV, MG, CL
Pockets
3 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
TDNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG) P*GP*CP*GP*CP*AP*TP*CP*AP*G)-3')dna16——
PDNA (5'-D(*CP*TP*GP*AP*TP*GP*CP*GP*CP*CP*T)-3')dna11——
DDNA (5'-D(P*GP*TP*CP*GP*G)-3')dna5——
ADNA polymerase beta (EC 2.7.7.7, 4.2.99.-)protein32750% helix, 13% strandP06746

Ligands and binding sites

  • TTP · Thymidine-5'-triphosphate · ligand · chains T, P, A
  • PPV · Pyrophosphate · ligand · chains P, A
  • MG · Magnesium ion · metal · 6 copies · chains T, P, A
  • CL · Chloride ion · ion · chains A
  • IMD · Imidazole · additive · 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
18940.700.7658MG, PPV
24110.640.7833empty
32580.600.8027empty

Interfaces

5 interfaces between chains.

  • T–A · 734 Ų buried · 16 hydrogen bonds · protein-nucleic
  • P–A · 537 Ų buried · 15 hydrogen bonds · protein-nucleic
  • T–P · 492 Ų buried · 43 hydrogen bonds · nucleic-nucleic
  • D–A · 379 Ų buried · 9 hydrogen bonds · protein-nucleic
  • T–D · 238 Ų buried · 23 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

  • 5VRY · Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 20 s · 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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