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MolNFT v1 · #42999 · protein + DNA

Klenow fragment with normal substrate and zinc only

2KZZ · DNA (5'-D(*GP*CP*TP*T*AP*CP*G)-3'): “Klenow fragment with normal substrate and zinc only”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.60). MolNFT v1 #42999 on GenesisL1: 3D structure, binding sites and pockets…

PDB
2KZZ
Type
protein + DNA
Length
603 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*GP*CP*TP*T*AP*CP*G)-3'); Protein (DNA polymerase I)
EC
2.7.7.7
UniProt
P00582
Ligands
ZN
Pockets
6 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BDNA (5'-D(*GP*CP*TP*T*AP*CP*G)-3')dna2——
AProtein (DNA polymerase I) (EC 2.7.7.7)protein60151% helix, 13% strandP00582

Ligands and binding sites

  • ZN · Zinc ion · metal · 3 copies · chains B, 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, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13000.600.7938empty
22950.500.7336empty
3960.360.7417empty
4860.360.7616empty
51020.350.7316empty

Interfaces

1 interface between chains.

  • B–A · 454 Ų buried · 10 hydrogen bonds · protein-nucleic

Compared structures

  • 2KZZ · Klenow fragment with normal substrate and zinc only · the same entry in another collection · chain A against A, 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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