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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
1KFS
Type
protein + DNA
Length
604 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*GP*CP*TP*TP*AP*CP*G)-3'); Protein (DNA polymerase I klenow fragment…
EC
2.7.7.7
UniProt
P00582
Ligands
ZN, MG
Pockets
7 · best druggability 0.52

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
BDNA (5'-D(*GP*CP*TP*TP*AP*CP*G)-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 · 3 copies · chains B, A
  • MG · Magnesium ion · metal · 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, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11460.520.8021empty
22280.480.7433ZN
3650.440.8319empty
41080.400.7618empty
51000.360.7417empty

Interfaces

1 interface between chains.

  • B–A · 648 Ų buried · 21 hydrogen bonds · protein-nucleic

Compared structures

  • 1KFS · 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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