MolNFT v1 · #124582 · protein
Synechocystis apocarotenoid oxygenase (aco) mutant - GLU150GLN
5KJD · Apocarotenoid-15,15'-oxygenase: “Synechocystis apocarotenoid oxygenase (aco) mutant - GLU150GLN”. X-ray diffraction, 1 ligand (FE2), 20 pockets (best druggability 0.87). MolNFT v1 #124582 on GenesisL1: 3D structure, binding sites…
- PDB
- 5KJD
- Type
- protein
- Length
- 2,395 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
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Apocarotenoid-15,15'-oxygenase (EC 1.13.11.75) | protein | 479 | 8% helix, 41% strand | P74334 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.87 | 0.88 | 94 | FE2 |
| 2 | 1200 | 0.86 | 0.87 | 103 | FE2 |
| 3 | 1083 | 0.86 | 0.86 | 84 | FE2 |
| 4 | 1137 | 0.85 | 0.86 | 85 | FE2 |
| 5 | 1075 | 0.85 | 0.86 | 83 | FE2 |
Interfaces
5 interfaces between chains.
- B–D · 573 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 552 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 427 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 271 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 145 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5KJD · Synechocystis apocarotenoid oxygenase (ACO) mutant - Glu150Gln · 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 5KJD · PDBe 5KJD · UniProt P74334
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