MolNFT v1 · #116674 · protein

C-terminal his tagged appol exonuclease mutant

5DKU · Prex DNA polymerase: “C-terminal his tagged appol exonuclease mutant”. X-ray diffraction, 1 ligand (MG), 19 pockets (best druggability 0.84). MolNFT v1 #116674 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DKU
Type: protein
Length: 1,158 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prex DNA polymerase
EC: 2.7.7.7
UniProt: Q8ILY1
Ligands: MG
Pockets: 19 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prex DNA polymerase (EC 2.7.7.7)	protein	577	50% helix, 17% strand	Q8ILY1
B	Prex DNA polymerase (EC 2.7.7.7)	protein	581	50% helix, 17% strand	Q8ILY1

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1020	0.84	0.84	89	empty
2	766	0.81	0.84	79	empty
3	583	0.70	0.78	57	MG
4	501	0.69	0.79	58	MG
5	59	0.52	0.87	17	empty

Interfaces

1 interface between chains.

A–B · 999 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5DKU · C-terminal His tagged apPOL exonuclease mutant · the same entry in another collection · chain A against A, TM-score 1.00

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 Q8ILY1
Elsewhere: RCSB PDB 5DKU · PDBe 5DKU · UniProt Q8ILY1

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