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Crystal structure of apocarotenoid cleavage oxygenase from synechocystis, native enzyme
Analyse Crystal structure of apocarotenoid cleavage oxygenase from synechocystis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BIW
- Type
- protein
- Length
- 1,916 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apocarotenoid-cleaving oxygenase
- UniProt
- P74334
- Ligands
- 3ON, FE
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Apocarotenoid-cleaving oxygenase | protein | 479 | 8% helix, 41% strand | P74334 |
Ligands and binding sites
- 3ON · (3R)-3-hydroxy-8'-apocarotenol · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.86 | 0.87 | 98 | 3ON |
| 2 | 1118 | 0.86 | 0.87 | 93 | 3ON |
| 3 | 1141 | 0.85 | 0.86 | 82 | 3ON |
| 4 | 1159 | 0.85 | 0.85 | 78 | 3ON |
| 5 | 416 | 0.80 | 0.88 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–C · 582 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 505 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 437 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2BIW · Crystal structure of apocarotenoid cleavage oxygenase from Synechocystis, native enzyme · the same entry in another collection · chain D against D, TM-score 1.00
- P74334 · AlphaFold monomer V2.0 prediction for apocarotenoid-15,15'-oxygenase (P74334) · a predicted model of the same protein · chain D 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 P74334
- Elsewhere: RCSB PDB 2BIW · PDBe 2BIW · UniProt P74334
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