Research workbench
Crystal structure of boxb with malonate bound to the diiron center
Analyse Crystal structure of boxb with malonate bound to the diiron center in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PF7
- Type
- protein
- Length
- 947 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzoyl-CoA oxygenase component B
- EC
- 1.14.12.21
- UniProt
- Q9AIX7
- Ligands
- FE, OH, CL
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Benzoyl-CoA oxygenase component B (EC 1.14.12.21) | protein | 477 | 53% helix, 8% strand | Q9AIX7 |
| B | Benzoyl-CoA oxygenase component B (EC 1.14.12.21) | protein | 470 | 52% helix, 8% strand | Q9AIX7 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- MLA · Malonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.70 | 0.85 | 39 | MLA |
| 2 | 273 | 0.66 | 0.82 | 37 | MLA |
| 3 | 267 | 0.52 | 0.75 | 27 | empty |
| 4 | 116 | 0.45 | 0.78 | 24 | empty |
| 5 | 141 | 0.40 | 0.74 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 101 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3PF7 · Crystal structure of BoxB with malonate bound to the diiron center · the same entry in another collection · chain A against A, TM-score 1.00
- Q9AIX7 · AlphaFold monomer V2.0 prediction for benzoyl-CoA oxygenase component B (Q9AIX7) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9AIX7
- Elsewhere: RCSB PDB 3PF7 · PDBe 3PF7 · UniProt Q9AIX7
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