MolNFT v1 · #34513 · protein
Crystal structure of the allene oxide cyclase 2 with bound inhibitor vernolic acid
2DIO: “Crystal structure of the allene oxide cyclase 2 with bound inhibitor vernolic acid”. X-ray diffraction, 1 ligand (EOD), 9 pockets (best druggability 0.71). MolNFT v1 #34513 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2DIO
- Type
- protein
- Length
- 522 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allene oxide cyclase 2
- EC
- 5.3.99.6
- UniProt
- Q9LS02
- Ligands
- EOD
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Allene oxide cyclase 2 (EC 5.3.99.6) | protein | 174 | 9% helix, 48% strand | Q9LS02 |
Ligands and binding sites
- EOD · 11-[(2R,3S)-3-pentyloxiran-2-yl]undecanoic acid · ligand · chains B
- GOL · Glycerol · additive · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.71 | 0.91 | 20 | empty |
| 2 | 108 | 0.71 | 0.91 | 20 | EOD |
| 3 | 133 | 0.69 | 0.89 | 23 | empty |
| 4 | 110 | 0.56 | 0.84 | 29 | empty |
| 5 | 265 | 0.53 | 0.76 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–C · 952 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 939 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 927 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 2DIO · Crystal Structure of the Allene Oxide Cyclase 2 with bound inhibitor vernolic acid · the same entry in another collection · chain A against A, TM-score 1.00
- Q9LS02 · AlphaFold monomer V2.0 prediction for allene oxide cyclase 2, chloroplastic (Q9LS02) · a predicted model of the same protein · chain C against A, TM-score 1.00
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 Q9LS02
- Elsewhere: RCSB PDB 2DIO · PDBe 2DIO · UniProt Q9LS02
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