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

Analyse DNA polymerase I klenow fragment (E.C.2.7.7.7) MUTANT/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1KSP
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
6 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 54% 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)protein60154% helix, 13% strandP00582

Ligands and binding sites

  • ZN · Zinc ion · metal · 2 copies · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11550.550.8123empty
23130.510.7338ZN
3970.390.7617empty
4890.370.7516empty
51030.350.7318empty

Interfaces

1 interface between chains.

  • B–A · 620 Ų buried · 11 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

  • 1KSP · 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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