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MolNFT v1 · #97666 · protein + DNA

DNA polymerase beta mismatched reactant complex with MN2+, 10 min

4KLS: “DNA polymerase beta mismatched reactant complex with MN2+, 10 min”. X-ray diffraction, 4 ligands (DTP, PPV, NA), 3 pockets (best druggability 0.73). MolNFT v1 #97666 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
4KLS
Type
protein + DNA
Length
356 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA polymerase beta; 5'-D(P*GP*TP*CP*GP*G)-3'; 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*A)-3'…
EC
2.7.7.7, 4.2.99.-
UniProt
P06746
Ligands
DTP, PPV, NA, MN
Pockets
3 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA polymerase beta (EC 2.7.7.7, 4.2.99.-)protein32452% helix, 13% strandP06746
D5'-D(P*GP*TP*CP*GP*G)-3'dna5——
P5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*A)-3'dna11——
T5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'dna16——

Ligands and binding sites

  • DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, P
  • PPV · Pyrophosphate · ligand · chains A, P
  • NA · Sodium ion · metal · 3 copies · chains A, P, D
  • MN · Manganese (II) ion · metal · 3 copies · chains A, P

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
17670.730.7972DTP, PPV, MN
23140.650.8127empty
32480.590.8025empty

Interfaces

5 interfaces between chains.

  • A–P · 592 Ų buried · 14 hydrogen bonds · protein-nucleic
  • P–T · 488 Ų buried · 39 hydrogen bonds · nucleic-nucleic
  • A–T · 480 Ų buried · 10 hydrogen bonds · protein-nucleic
  • A–D · 382 Ų buried · 10 hydrogen bonds · protein-nucleic
  • D–T · 231 Ų buried · 24 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

  • 4KLS · DNA polymerase beta mismatched reactant complex with Mn2+, 10 min · 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 0.96

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