MolNFT v1 · #122252 · protein

D-family DNA polymerase - DP2 subunit (catalytic subunit)

5IJL · DNA polymerase II large subunit: “D-family DNA polymerase - DP2 subunit (catalytic subunit)”. X-ray diffraction, 1 ligand (ZN), 13 pockets (best druggability 0.64). MolNFT v1 #122252 on GenesisL1: 3D structure, binding sites and…

PDB: 5IJL
Type: protein
Length: 943 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase II large subunit
EC: 2.7.7.7
UniProt: Q9V2F4
Ligands: ZN
Pockets: 13 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase II large subunit (EC 2.7.7.7)	protein	943	41% helix, 17% strand	Q9V2F4

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

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	622	0.64	0.75	41	empty
2	484	0.63	0.76	53	empty
3	160	0.61	0.84	23	empty
4	171	0.53	0.79	36	empty
5	167	0.50	0.77	25	empty

Compared structures

5IJL · D-family DNA polymerase - DP2 subunit (catalytic subunit) · the same entry in another collection · chain A against A, TM-score 1.00
Q9V2F4 · AlphaFold monomer V2.0 prediction for DNA polymerase II large subunit (Q9V2F4) · a predicted model of the same protein · chain A against A, TM-score 0.74

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9V2F4
Elsewhere: RCSB PDB 5IJL · PDBe 5IJL · UniProt Q9V2F4

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