Research workbench

M64V pnp + allo

Analyse M64V pnp + allo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1OV6
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: DBM, PO4
Pockets: 7 · best druggability 0.64

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

DBM · 9-(6-deoxy-beta-D-allofuranosyl)-6-methylpurine · ligand · 3 copies · chains A, B, C
PO4 · Phosphate ion · ion · 3 copies · chains A, B, C

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	306	0.64	0.80	47	PO4, DBM
2	312	0.57	0.76	42	PO4, DBM
3	217	0.52	0.76	37	PO4, DBM
4	138	0.39	0.73	18	empty
5	81	0.32	0.74	16	empty

Interfaces

3 interfaces between chains.

A–B · 123 Å² buried · 1 hydrogen bond · protein-protein
B–C · 118 Å² buried · 1 hydrogen bond · protein-protein
A–C · 117 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1OV6 · M64V pnp + allo · the same entry in another collection · chain A against A, 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 1OV6 · PDBe 1OV6 · UniProt P0ABP8

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