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Crystal structure of human pnp complexed with immucillin H

Analyse Crystal structure of human pnp complexed with immucillin H in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PF7
Type: protein
Length: 288 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Purine nucleoside phosphorylase
EC: 2.4.2.1
UniProt: P00491
Ligands: IMH, SO4
Pockets: 2 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Purine nucleoside phosphorylase (EC 2.4.2.1)	protein	288	34% helix, 23% strand	P00491

Ligands and binding sites

IMH · 1,4-dideoxy-4-aza-1-(S)-(9-deazahypoxanthin-9-yl)-D-ribitol · ligand · chains E
SO4 · Sulfate ion · ion · 3 copies · chains E

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	306	0.62	0.79	52	SO4, IMH
2	56	0.25	0.72	12	empty

Compared structures

1PF7 · Crystal structure of human pnp complexed with immucillin H · the same entry in another collection · chain E against E, TM-score 1.00
P00491 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (P00491) · a predicted model of the same protein · chain E against A, TM-score 0.95

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 P00491
Elsewhere: RCSB PDB 1PF7 · PDBe 1PF7 · UniProt P00491

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