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Structure of human pnp complexed with ddi

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

PDB: 1V3Q
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: 2DI, SO4
Pockets: 1 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Purine nucleoside phosphorylase (EC 2.4.2.1)	protein	288	33% helix, 23% strand	P00491

Ligands and binding sites

2DI · 9-[(2R,5R)-5-(hydroxymethyl)tetrahydrofuran-2-yl]-1,9-dihydro-6H-purin-6-one · 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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	304	0.64	0.81	46	SO4, 2DI

Compared structures

1V3Q · Structure of human PNP complexed with DDI · 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 0.96

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 1V3Q · PDBe 1V3Q · UniProt P00491

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