MolNFT v2 · #172721 · protein

NUDIX1 hydrolase from Rosa x hybrida

6YPB · Geranyl diphosphate phosphohydrolase: “NUDIX1 hydrolase from Rosa x hybrida”. X-ray diffraction at 1.7, 1 pocket (best druggability 0.66). MolNFT v2 #172721 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YPB
Type: protein
Length: 130 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.7
Source: Rosa hybrid cultivar
Molecule: Geranyl diphosphate phosphohydrolase
EC: 3.6.1.68
UniProt: M4I1C6
Pockets: 1 · best druggability 0.66

Structure

x-ray diffraction · resolution 1.7 · 1 distinct chain · 18% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Geranyl diphosphate phosphohydrolase (EC 3.6.1.68)	protein	130	18% helix, 45% strand	M4I1C6

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	201	0.66	0.85	28	empty

Compared structures

6YPB · NUDIX1 hydrolase from rosa X hybrida · the same entry in another collection · chain A against A, TM-score 1.00
M4I1C6 · AlphaFold monomer V2.0 prediction for geranyl diphosphate phosphohydrolase (M4I1C6) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 M4I1C6
Elsewhere: RCSB PDB 6YPB · PDBe 6YPB · UniProt M4I1C6

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