MolNFT v1 · #137493 · protein
Crystal structure of rifampin monooxygenase from streptomyces venezuelae, complex with FAD
5VQB: “Crystal structure of rifampin monooxygenase from streptomyces venezuelae, complex with FAD”. X-ray diffraction, 2 ligands (FAD, CL), 14 pockets (best druggability 0.80). MolNFT v1 #137493 on GenesisL1: 3D structure, binding sites…
- PDB
- 5VQB
- Type
- protein
- Length
- 1,398 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rifampin monooxygenase
- UniProt
- F2R776
- Ligands
- FAD, CL
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rifampin monooxygenase | protein | 474 | 32% helix, 20% strand | F2R776 |
| B | Rifampin monooxygenase | protein | 460 | 33% helix, 19% strand | F2R776 |
| C | Rifampin monooxygenase | protein | 464 | 32% helix, 20% strand | F2R776 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 8 copies · chains A, B, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.80 | 0.82 | 96 | FAD |
| 2 | 1181 | 0.80 | 0.81 | 103 | FAD |
| 3 | 1101 | 0.78 | 0.80 | 94 | FAD |
| 4 | 689 | 0.71 | 0.78 | 65 | CL |
| 5 | 327 | 0.65 | 0.81 | 48 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1114 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 532 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5VQB · Crystal structure of rifampin monooxygenase from Streptomyces venezuelae, complex with FAD · the same entry in another collection · chain A against A, TM-score 1.00
- F2R776 · AlphaFold monomer V2.0 prediction for rifampicin monooxygenase (F2R776) · 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 F2R776
- Elsewhere: RCSB PDB 5VQB · PDBe 5VQB · UniProt F2R776
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