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Crystal structure of H. pylori purine nucleoside phosphorylase in complex with formycin a

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

PDB: 6F4W
Type: protein
Length: 1,398 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Purine nucleoside phosphorylase deod-type
EC: 2.4.2.1
UniProt: P56463
Ligands: FMC
Pockets: 14 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Purine nucleoside phosphorylase deod-type (EC 2.4.2.1)	protein	233	34% helix, 29% strand	P56463

Ligands and binding sites

FMC · (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol · ligand · 6 copies · chains A, D, B, E, C, F

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

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	821	0.75	0.79	76	empty
2	443	0.72	0.82	53	FMC
3	450	0.72	0.82	57	FMC
4	460	0.71	0.81	50	FMC
5	488	0.71	0.80	53	FMC

Interfaces

12 interfaces between chains.

C–E · 1835 Å² buried · 33 hydrogen bonds · protein-protein
A–F · 1805 Å² buried · 32 hydrogen bonds · protein-protein
B–D · 1803 Å² buried · 32 hydrogen bonds · protein-protein
C–F · 1695 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 1684 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6F4W · Crystal structure of H. pylori purine nucleoside phosphorylase in complex with formycin A · the same entry in another collection · chain E against E, TM-score 1.00
P56463 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (P56463) · a predicted model of the same protein · chain E against A, TM-score 0.99

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 P56463
Elsewhere: RCSB PDB 6F4W · PDBe 6F4W · UniProt P56463

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