Research workbench
X-ray structure of the wt allene oxide cyclase 2 from arabidopsis thaliana
Analyse X-ray structure of the wt allene oxide cyclase 2 from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GIN
- Type
- protein
- Length
- 1,038 residues
- Chains
- 6
- 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
- NA
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Allene oxide cyclase 2 (EC 5.3.99.6) | protein | 173 | 9% helix, 48% strand | Q9LS02 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.77 | 0.80 | 71 | GOL |
| 2 | 51 | 0.71 | 0.99 | 22 | empty |
| 3 | 50 | 0.71 | 0.99 | 18 | empty |
| 4 | 89 | 0.69 | 0.93 | 21 | empty |
| 5 | 132 | 0.68 | 0.88 | 20 | empty |
Interfaces
8 interfaces between chains.
- D–F · 993 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 952 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 945 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 939 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 932 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2GIN · X-ray structure of the wt allene oxide cyclase 2 from arabidopsis thaliana · the same entry in another collection · chain F against F, 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 F 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 2GIN · PDBe 2GIN · UniProt Q9LS02
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