Research workbench
Crystal structure of the allene oxide cyclase 2 from physcomitrella patens
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
- 4H6A
- 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
- A9RB27
- Ligands
- SO4
- Pockets
- 19 · best druggability 0.78
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 | 194 | 15% helix, 42% strand | A9RB27 |
| B | Allene oxide cyclase (EC 5.3.99.6) | protein | 180 | 16% helix, 45% strand | A9RB27 |
| C | Allene oxide cyclase (EC 5.3.99.6) | protein | 181 | 16% helix, 45% strand | A9RB27 |
| D | Allene oxide cyclase (EC 5.3.99.6) | protein | 179 | 16% helix, 45% strand | A9RB27 |
| E | Allene oxide cyclase (EC 5.3.99.6) | protein | 193 | 13% helix, 42% strand | A9RB27 |
| F | Allene oxide cyclase (EC 5.3.99.6) | protein | 180 | 15% helix, 46% strand | A9RB27 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B, D
- IPA · Isopropyl alcohol · additive · 7 copies · chains A, B, E, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, C, D
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.78 | 0.97 | 19 | MPD |
| 2 | 97 | 0.77 | 0.97 | 21 | MPD |
| 3 | 139 | 0.68 | 0.88 | 20 | IPA |
| 4 | 190 | 0.66 | 0.85 | 25 | IPA |
| 5 | 145 | 0.66 | 0.87 | 22 | MRD, IPA |
Interfaces
7 interfaces between chains.
- A–B · 1071 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1032 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 987 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 854 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 820 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4H6A · Crystal Structure of the Allene Oxide Cyclase 2 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 A9RB27
- Elsewhere: RCSB PDB 4H6A · PDBe 4H6A · UniProt A9RB27
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