Research workbench

NUDIX1 hydrolase from rosa X hybrida in complex with geranyl pyrophosphate

Analyse NUDIX1 hydrolase from rosa X hybrida in complex with geranyl pyrophosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YPF
Type: protein
Length: 129 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Geranyl diphosphate phosphohydrolase
EC: 3.6.1.68
UniProt: M4I1C6
Ligands: GPP
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Geranyl diphosphate phosphohydrolase (EC 3.6.1.68)	protein	129	19% helix, 43% strand	M4I1C6

Ligands and binding sites

GPP · Geranyl diphosphate · ligand · chains A

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	210	0.65	0.83	32	GPP

Compared structures

6YPF · NUDIX1 hydrolase from Rosa x hybrida in complex with geranyl pyrophosphate · 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 6YPF · PDBe 6YPF · UniProt M4I1C6

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.