MolNFT v1 · #17471 · protein

M64V pnp +talo

1OUM · Purine nucleoside phosphorylase: “M64V pnp +talo”. X-ray diffraction, 2 ligands (TAL, PO4), 8 pockets (best druggability 0.57). MolNFT v1 #17471 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1OUM
Type: protein
Length: 711 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Purine nucleoside phosphorylase
EC: 2.4.2.1
UniProt: P0ABP8
Ligands: TAL, PO4
Pockets: 8 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Purine nucleoside phosphorylase (EC 2.4.2.1)	protein	237	35% helix, 28% strand	P0ABP8

Ligands and binding sites

TAL · 9-(6-deoxy-alpha-L-talofuranosyl)-6-methylpurine · ligand · 3 copies · chains A, B, C
PO4 · Phosphate ion · ion · 2 copies · chains B, C

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	256	0.57	0.78	38	PO4, TAL
2	215	0.54	0.77	37	PO4, TAL
3	147	0.48	0.78	27	TAL
4	139	0.40	0.74	18	empty
5	65	0.33	0.77	16	empty

Interfaces

3 interfaces between chains.

A–B · 133 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 114 Å² buried · 1 hydrogen bond · protein-protein
A–C · 111 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1OUM · M64V PNP +Talo · the same entry in another collection · chain B against B, TM-score 1.00
P0ABP8 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (P0ABP8) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P0ABP8
Elsewhere: RCSB PDB 1OUM · PDBe 1OUM · UniProt P0ABP8

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