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MolNFT v1 · #12787 · protein + DNA

DNA polymerase I klenow fragment (E.C.2.7.7.7) MUTANT/DNA complex

1KRP · DNA (5'-D(P*TP*TP*PST)-3'): “DNA polymerase I klenow fragment (E.C.2.7.7.7) MUTANT/DNA complex”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.54). MolNFT v1 #12787 on GenesisL1: 3D structure, binding sites and…

PDB
1KRP
Type
protein + DNA
Length
604 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(P*TP*TP*PST)-3'); Protein (DNA polymerase I klenow fragment (E.C.2.7.7.7))
EC
2.7.7.7
UniProt
P00582
Ligands
ZN
Pockets
7 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BDNA (5'-D(P*TP*TP*PST)-3')dna3——
AProtein (DNA polymerase I klenow fragment (E.C.2.7.7.7)) (EC 2.7.7.7)protein60152% helix, 13% strandP00582

Ligands and binding sites

  • ZN · Zinc ion · metal · 4 copies · chains B, A

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11440.540.8123empty
23240.520.7342ZN
3520.450.8520empty
4960.370.7516empty
5950.370.7617empty

Interfaces

1 interface between chains.

  • B–A · 617 Ų buried · 14 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

  • 1KRP · DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex · the same entry in another collection · chain B against B, TM-score 1.00
  • P00582 · AlphaFold monomer V2.0 prediction for DNA polymerase I (P00582) · a predicted model of the same protein · chain A against A, TM-score 0.95

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