MolNFT v1 · #177499 · protein
Crystal structure of gibberellin 3-oxidase 2 (GA3OX2) in rice
7EKD · Gibberellin 3-beta-dioxygenase 2: “Crystal structure of gibberellin 3-oxidase 2 (GA3OX2) in rice”. X-ray diffraction, 3 ligands (AKG, J5X, PO4), 5 pockets (best druggability 0.76). MolNFT v1 #177499 on GenesisL1: 3D structure…
- PDB
- 7EKD
- Type
- protein
- Length
- 343 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gibberellin 3-beta-dioxygenase 2
- EC
- 1.14.11.15
- UniProt
- Q9FU53
- Ligands
- AKG, J5X, PO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gibberellin 3-beta-dioxygenase 2 (EC 1.14.11.15) | protein | 343 | 38% helix, 20% strand | Q9FU53 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- J5X · Gibberellin A9 · ligand · chains A
- PO4 · Phosphate ion · ion · 4 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.76 | 0.84 | 47 | AKG, MPD, J5X |
| 2 | 287 | 0.54 | 0.75 | 34 | PO4 |
| 3 | 56 | 0.45 | 0.84 | 16 | empty |
| 4 | 118 | 0.39 | 0.75 | 21 | empty |
| 5 | 76 | 0.32 | 0.74 | 18 | empty |
Compared structures
- 7EKD · Crystal structure of gibberellin 3-oxidase 2 (GA3ox2) in rice · the same entry in another collection · chain A against A, TM-score 1.00
- Q9FU53 · AlphaFold monomer V2.0 prediction for gibberellin 3-beta-dioxygenase 2 (Q9FU53) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9FU53
- Elsewhere: RCSB PDB 7EKD · PDBe 7EKD · UniProt Q9FU53
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.