Research workbench
Crystal structure of the allene oxide cyclase 1 from physcomitrella patens
Analyse Crystal structure of the allene oxide cyclase 1 from physcomitrella patens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H6C
- Type
- protein
- Length
- 2,127 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allene oxide cyclase
- EC
- 5.3.99.6
- UniProt
- Q8GS38
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, I, K | Allene oxide cyclase (EC 5.3.99.6) | protein | 180 | 7% helix, 46% strand | Q8GS38 |
| C | Allene oxide cyclase (EC 5.3.99.6) | protein | 175 | 7% helix, 47% strand | Q8GS38 |
| B | Allene oxide cyclase (EC 5.3.99.6) | protein | 177 | 7% helix, 47% strand | Q8GS38 |
| F, G, H, J | Allene oxide cyclase (EC 5.3.99.6) | protein | 175 | 7% helix, 46% strand | Q8GS38 |
| L | Allene oxide cyclase (EC 5.3.99.6) | protein | 175 | 7% helix, 46% strand | Q8GS38 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 17 copies · chains A, D, C, B, E, F, G, H, I, J, K, L
- HEZ · Hexane-1,6-diol · additive · 6 copies · chains A, D, E, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.73 | 0.81 | 66 | HEZ |
| 2 | 412 | 0.71 | 0.82 | 49 | empty |
| 3 | 127 | 0.70 | 0.90 | 22 | empty |
| 4 | 174 | 0.69 | 0.87 | 25 | empty |
| 5 | 156 | 0.69 | 0.88 | 25 | empty |
Interfaces
18 interfaces between chains.
- B–F · 879 Ų buried · 9 hydrogen bonds · protein-protein
- K–L · 879 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 874 Ų buried · 9 hydrogen bonds · protein-protein
- D–C · 874 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 872 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4H6C · Crystal Structure of the Allene Oxide Cyclase 1 from Physcomitrella patens · the same entry in another collection · 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 Q8GS38
- Elsewhere: RCSB PDB 4H6C · PDBe 4H6C · UniProt Q8GS38
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