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MolNFT v1 · #70430 · protein + DNA

DNA polymerase beta with a gapped DNA substrate and DTMP(CF2)P(CF2)P

3LK9: “DNA polymerase beta with a gapped DNA substrate and DTMP(CF2)P(CF2)P”. X-ray diffraction, 4 ligands (TFF, MG, NA), 3 pockets (best druggability 0.71). MolNFT v1 #70430 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
3LK9
Type
protein + DNA
Length
357 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA polymerase beta; DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
EC
2.7.7.7, 4.2.99.-
UniProt
P06746
Ligands
TFF, MG, NA, CL
Pockets
3 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA polymerase beta (EC 2.7.7.7, 4.2.99.-)protein32648% helix, 14% strandP06746
TDNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3')dna16——
PDNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')dna10——
DDNA (5'-D(P*GP*TP*CP*GP*G)-3')dna5——

Ligands and binding sites

  • TFF · 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl](difluoro)methyl}(hydroxy)phosphoryl]thymidine · ligand · chains A, T, P
  • MG · Magnesium ion · metal · 2 copies · chains A, P
  • NA · Sodium ion · metal · 2 copies · chains A, P, D
  • 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
110150.710.7666TFF, MG
23590.640.7929empty
32030.570.8026empty

Interfaces

5 interfaces between chains.

  • A–T · 725 Ų buried · 16 hydrogen bonds · protein-nucleic
  • T–P · 468 Ų buried · 50 hydrogen bonds · nucleic-nucleic
  • A–D · 398 Ų buried · 9 hydrogen bonds · protein-nucleic
  • A–P · 366 Ų buried · 10 hydrogen bonds · protein-nucleic
  • T–D · 230 Ų buried · 24 hydrogen bonds · nucleic-nucleic

Compared structures

  • 3LK9 · DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P · the same entry in another collection · chain A against A, 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 0.95

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