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Crystal structure of a nucleoside triphosphate diphosphohydrolase (ntpdase) from the legume trifolium repens

Analyse Crystal structure of a nucleoside triphosphate diphosphohydrolase (ntpdase)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5U7P
Type: protein
Length: 405 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apyrase
EC: 3.6.1.5
UniProt: B9U139
Ligands: PO4
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apyrase (EC 3.6.1.5)	protein	405	37% helix, 26% strand	B9U139

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A

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

Pockets

3 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	373	0.56	0.75	48	PO4
2	72	0.34	0.76	23	empty
3	52	0.27	0.74	15	empty

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5U7P · Crystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the… · 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 B9U139
Elsewhere: RCSB PDB 5U7P · PDBe 5U7P · UniProt B9U139

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