Research workbench
Crystal structure of gibberellin 2-OXIDASE3 (GA2OX3)IN rice
Analyse Crystal structure of gibberellin 2-OXIDASE3 (GA2OX3)IN rice in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KU3
- Type
- protein
- Length
- 1,262 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gibberellin 2-beta-dioxygenase 3
- EC
- 1.14.11.13
- UniProt
- Q8S0S6
- Ligands
- GA4, AKG, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gibberellin 2-beta-dioxygenase 3 (EC 1.14.11.13) | protein | 317 | 28% helix, 28% strand | Q8S0S6 |
| B | Gibberellin 2-beta-dioxygenase 3 (EC 1.14.11.13) | protein | 318 | 28% helix, 29% strand | Q8S0S6 |
| C | Gibberellin 2-beta-dioxygenase 3 (EC 1.14.11.13) | protein | 317 | 29% helix, 27% strand | Q8S0S6 |
| D | Gibberellin 2-beta-dioxygenase 3 (EC 1.14.11.13) | protein | 310 | 30% helix, 30% strand | Q8S0S6 |
Ligands and binding sites
- GA4 · Gibberellin A4 · ligand · 6 copies · chains A, D, B, C
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.88 | 0.89 | 121 | GA4, AKG, GOL |
| 2 | 1180 | 0.87 | 0.88 | 117 | GA4, AKG, SO4 |
| 3 | 353 | 0.59 | 0.77 | 35 | empty |
| 4 | 331 | 0.57 | 0.76 | 35 | empty |
| 5 | 134 | 0.45 | 0.76 | 22 | GOL |
Interfaces
4 interfaces between chains.
- B–C · 618 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 616 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 341 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 308 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6KU3 · Crystal structure of gibberellin 2-oxidase3 (GA2ox3)in rice · the same entry in another collection · chain D against D, TM-score 1.00
- Q8S0S6 · AlphaFold monomer V2.0 prediction for gibberellin 2-beta-dioxygenase 3 (Q8S0S6) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q8S0S6
- Elsewhere: RCSB PDB 6KU3 · PDBe 6KU3 · UniProt Q8S0S6
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