Research workbench
Complex of the heme and FMN-binding domains of the cytochrome P450(BM-3)
Analyse Complex of the heme and FMN-binding domains of the cytochrome P450(BM-3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BVY
- Type
- protein
- Length
- 1,029 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (cytochrome P450 bm-3)
- EC
- 1.14.14.1
- UniProt
- P14779
- Ligands
- HEM, FMN
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (cytochrome P450 bm-3) (EC 1.14.14.1) | protein | 439 | 55% helix, 11% strand | P14779 |
| F | Protein (cytochrome P450 bm-3) (EC 1.14.14.1) | protein | 152 | 38% helix, 21% strand | P14779 |
| B | Protein (cytochrome P450 bm-3) (EC 1.14.14.1) | protein | 438 | 55% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · chains A, F
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, F, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.88 | 0.92 | 99 | HEM, EDO |
| 2 | 1073 | 0.82 | 0.83 | 102 | HEM, EDO |
| 3 | 238 | 0.75 | 0.89 | 44 | FMN |
| 4 | 448 | 0.66 | 0.78 | 50 | empty |
| 5 | 325 | 0.55 | 0.75 | 41 | EDO |
Interfaces
2 interfaces between chains.
- A–B · 1069 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 795 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1BVY · Complex of the heme and FMN-binding domains of the cytochrome P450(BM-3) · the same entry in another collection · chain A against A, TM-score 1.00
- P14779 · AlphaFold monomer V2.0 prediction for bifunctional cytochrome P450/NADPH--P450 reductase… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P14779
- Elsewhere: RCSB PDB 1BVY · PDBe 1BVY · UniProt P14779
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