MolNFT v1 · #75300 · protein
Crystal structure of boxb in mixed valent state with bound benzoyl-CoA
3PM5 · Benzoyl-CoA oxygenase component B: “Crystal structure of boxb in mixed valent state with bound benzoyl-CoA”. X-ray diffraction, 4 ligands (BYC, FE, SO4), 19 pockets (best druggability 0.84). MolNFT v1 #75300 on GenesisL1: 3D…
- PDB
- 3PM5
- Type
- protein
- Length
- 1,886 residues
- Chains
- 4
- 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
- BYC, FE, SO4, CL
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Benzoyl-CoA oxygenase component B (EC 1.14.12.21) | protein | 472 | 51% helix, 9% strand | Q9AIX7 |
| B | Benzoyl-CoA oxygenase component B (EC 1.14.12.21) | protein | 470 | 52% helix, 9% strand | Q9AIX7 |
| C | Benzoyl-CoA oxygenase component B (EC 1.14.12.21) | protein | 475 | 51% helix, 9% strand | Q9AIX7 |
| D | Benzoyl-CoA oxygenase component B (EC 1.14.12.21) | protein | 469 | 52% helix, 9% strand | Q9AIX7 |
Ligands and binding sites
- BYC · benzoyl coenzyme A · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- PGO · S-1,2-propanediol · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains C, D
- PGE · Triethylene glycol · additive · chains C, D
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 | 624 | 0.84 | 0.89 | 96 | CL, BYC |
| 2 | 468 | 0.83 | 0.90 | 70 | SO4, CL, FE, BYC |
| 3 | 543 | 0.83 | 0.88 | 78 | BYC, CL, PGO, PGE |
| 4 | 497 | 0.82 | 0.89 | 76 | SO4, CL, FE, BYC |
| 5 | 103 | 0.62 | 0.88 | 25 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1232 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1222 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 781 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3PM5 · Crystal Structure of BoxB in mixed valent state with bound benzoyl-CoA · the same entry in another collection · chain D against D, 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 D 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 3PM5 · PDBe 3PM5 · UniProt Q9AIX7
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