MolNFT v1 · #129617 · protein

Crystal structure of K25E cn-II mutant

5OPL · Cytosolic purine 5'-nucleotidase: “Crystal structure of K25E cn-II mutant”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.70). MolNFT v1 #129617 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5OPL
Type: protein
Length: 470 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytosolic purine 5'-nucleotidase
EC: 3.1.3.5
UniProt: P49902
Ligands: MG
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytosolic purine 5'-nucleotidase (EC 3.1.3.5)	protein	470	44% helix, 18% strand	P49902

Ligands and binding sites

MG · Magnesium ion · metal · chains A
GOL · Glycerol · additive · 9 copies · chains A

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

Pockets

5 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	117	0.70	0.92	27	empty
2	183	0.63	0.84	23	GOL
3	344	0.62	0.78	42	GOL
4	312	0.58	0.77	27	empty
5	145	0.50	0.78	16	empty

Compared structures

5OPL · Crystal structure of K25E cN-II mutant · the same entry in another collection · chain A against A, TM-score 1.00
P49902 · AlphaFold monomer V2.0 prediction for cytosolic purine 5'-nucleotidase (P49902) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P49902
Elsewhere: RCSB PDB 5OPL · PDBe 5OPL · UniProt P49902

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