Research workbench
Synechocystis apocarotenoid oxygenase (aco) mutant - TRP149ALA
Analyse Synechocystis apocarotenoid oxygenase (aco) mutant - TRP149ALA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KJA
- Type
- protein
- Length
- 2,398 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apocarotenoid-15,15'-oxygenase
- EC
- 1.13.11.75
- UniProt
- P74334
- Ligands
- FE2, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apocarotenoid-15,15'-oxygenase (EC 1.13.11.75) | protein | 482 | 9% helix, 42% strand | P74334 |
| B, C, D, E | Apocarotenoid-15,15'-oxygenase (EC 1.13.11.75) | protein | 479 | 9% helix, 43% strand | P74334 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 5 copies · chains A, B, C, D, E
- CL · Chloride ion · ion · 2 copies · chains A, C, B, 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 | 897 | 0.87 | 0.88 | 88 | FE2 |
| 2 | 1058 | 0.86 | 0.86 | 90 | FE2 |
| 3 | 1098 | 0.85 | 0.86 | 98 | FE2 |
| 4 | 1149 | 0.85 | 0.86 | 97 | CL, FE2 |
| 5 | 970 | 0.85 | 0.86 | 90 | FE2 |
Interfaces
5 interfaces between chains.
- A–C · 674 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 608 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 445 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 279 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 125 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5KJA · Synechocystis apocarotenoid oxygenase (ACO) mutant - Trp149Ala · the same entry in another collection · chain E against E, TM-score 1.00
- P74334 · AlphaFold monomer V2.0 prediction for apocarotenoid-15,15'-oxygenase (P74334) · a predicted model of the same protein · 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 P74334
- Elsewhere: RCSB PDB 5KJA · PDBe 5KJA · UniProt P74334
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