MolNFT v1 · #146251 · protein
Crystal structure of nudix 1 from arabidopsis thaliana complexed with isopentenyl diphosphate
6DBZ · Nudix hydrolase 1: “Crystal structure of nudix 1 from arabidopsis thaliana complexed with isopentenyl diphosphate”. X-ray diffraction, 2 ligands (IPR, MG), 4 pockets (best druggability 0.71). MolNFT v1 #146251 on GenesisL1: 3D…
- PDB
- 6DBZ
- Type
- protein
- Length
- 276 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nudix hydrolase 1
- EC
- 3.6.1.55, 3.6.1.67, 3.6.1.22
- UniProt
- Q9CA40
- Ligands
- IPR, MG
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nudix hydrolase 1 (EC 3.6.1.55, 3.6.1.67, 3.6.1.22) | protein | 138 | 17% helix, 41% strand | Q9CA40 |
Ligands and binding sites
- IPR · Isopentyl pyrophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.71 | 0.85 | 36 | IPR, MG |
| 2 | 282 | 0.71 | 0.85 | 35 | IPR, MG |
| 3 | 102 | 0.37 | 0.75 | 19 | empty |
| 4 | 61 | 0.30 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 928 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6DBZ · Crystal structure of Nudix 1 from Arabidopsis thaliana complexed with isopentenyl… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9CA40 · AlphaFold monomer V2.0 prediction for nudix hydrolase 1 (Q9CA40) · 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 Q9CA40
- Elsewhere: RCSB PDB 6DBZ · PDBe 6DBZ · UniProt Q9CA40
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