Research workbench
Crystal structure of the allene oxide cyclase 2 from physcomitrella patens complexed with substrate analog
Analyse Crystal structure of the allene oxide cyclase 2 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
- 4H69
- Type
- protein
- Length
- 1,107 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allene oxide cyclase
- EC
- 5.3.99.6
- UniProt
- Q8H0N6
- Ligands
- 10Y, PO4
- Pockets
- 18 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Allene oxide cyclase (EC 5.3.99.6) | protein | 190 | 15% helix, 41% strand | Q8H0N6 |
| B | Allene oxide cyclase (EC 5.3.99.6) | protein | 180 | 16% helix, 44% strand | Q8H0N6 |
| C | Allene oxide cyclase (EC 5.3.99.6) | protein | 180 | 16% helix, 45% strand | Q8H0N6 |
| D | Allene oxide cyclase (EC 5.3.99.6) | protein | 180 | 16% helix, 46% strand | Q8H0N6 |
| E | Allene oxide cyclase (EC 5.3.99.6) | protein | 193 | 13% helix, 42% strand | Q8H0N6 |
| F | Allene oxide cyclase (EC 5.3.99.6) | protein | 184 | 15% helix, 45% strand | Q8H0N6 |
Ligands and binding sites
- 10Y · (9Z)-11-{(2R,3S)-3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}undec-9-enoic acid · ligand · 5 copies · chains A, B, C, D, F
- PO4 · Phosphate ion · ion · 2 copies · chains A, D
- IPA · Isopropyl alcohol · additive · 4 copies · chains A, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.69 | 0.89 | 22 | 10Y |
| 2 | 151 | 0.68 | 0.87 | 26 | 10Y |
| 3 | 203 | 0.66 | 0.84 | 26 | empty |
| 4 | 151 | 0.66 | 0.86 | 21 | 10Y |
| 5 | 186 | 0.63 | 0.83 | 26 | 10Y |
Interfaces
7 interfaces between chains.
- A–D · 1106 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1065 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1064 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 862 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 854 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4H69 · Crystal Structure of the Allene Oxide Cyclase 2 from Physcomitrella patens complexed with… · 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 Q8H0N6
- Elsewhere: RCSB PDB 4H69 · PDBe 4H69 · UniProt Q8H0N6
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