MolNFT v1 · #88287 · protein
The crystal structure of the allene oxide cyclase 2 from arabidopsis thaliana with bound inhibitor - vernolic acid
4CQ6 · Allene oxide cyclase 2, chloroplastic: “The crystal structure of the allene oxide cyclase 2 from arabidopsis thaliana with bound inhibitor - vernolic…”. X-ray diffraction, 2 ligands (T25, PO4), 10 pockets (best druggability 0.72).…
- PDB
- 4CQ6
- Type
- protein
- Length
- 522 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allene oxide cyclase 2, chloroplastic
- EC
- 5.3.99.6
- UniProt
- Q9LS02
- Ligands
- T25, PO4
- Pockets
- 10 · best druggability 0.72
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, chloroplastic (EC 5.3.99.6) | protein | 174 | 9% helix, 48% strand | Q9LS02 |
Ligands and binding sites
- T25 · (9Z)-11-[(2R,3S)-3-pentyloxiran-2-yl]undec-9-enoic acid · ligand · 2 copies · chains B, C
- PO4 · Phosphate ion · ion · chains A, C
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.72 | 0.91 | 21 | T25 |
| 2 | 119 | 0.70 | 0.91 | 21 | T25 |
| 3 | 129 | 0.67 | 0.88 | 22 | MRD |
| 4 | 94 | 0.55 | 0.85 | 29 | empty |
| 5 | 180 | 0.49 | 0.77 | 27 | empty |
Interfaces
3 interfaces between chains.
- B–C · 948 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 941 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 931 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4CQ6 · The crystal structure of the allene oxide cyclase 2 from Arabidopsis thaliana with bound… · 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 A 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 4CQ6 · PDBe 4CQ6 · UniProt Q9LS02
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