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Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate hppnp-3

Analyse Crystal structure of H. pylori purine nucleoside phosphorylase from clinical… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MX8
Type: protein
Length: 233 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Purine nucleoside phosphorylase deod-type
EC: 2.4.2.1
UniProt: K2JXG0
Ligands: HPA, PO4
Pockets: 2 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Purine nucleoside phosphorylase deod-type (EC 2.4.2.1)	protein	233	34% helix, 30% strand	K2JXG0

Ligands and binding sites

HPA · Hypoxanthine · ligand · chains A
PO4 · Phosphate ion · ion · chains A
PG4 · Tetraethylene glycol · additive · 8 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	248	0.59	0.79	35	HPA, PO4
2	55	0.30	0.76	13	empty

Compared structures

5MX8 · Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate… · 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 K2JXG0
Elsewhere: RCSB PDB 5MX8 · PDBe 5MX8 · UniProt K2JXG0

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