MolNFT v1 · #170994 · protein
NUDIX1 hydrolase from rosa X hybrida in complex with geranyl pyrophosphate
6YPF · Geranyl diphosphate phosphohydrolase: “NUDIX1 hydrolase from rosa X hybrida in complex with geranyl pyrophosphate”. X-ray diffraction, 1 ligand (GPP), 1 pocket (best druggability 0.65). MolNFT v1 #170994 on GenesisL1: 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.
| Volume (ų) | 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
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