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Crystal Structure of P450BM3 with N-perfluorodecanoyl-L-tryptophan
Analyse Crystal Structure of P450BM3 with N-perfluorodecanoyl-L-tryptophan in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B2Y
- Type
- protein
- Length
- 904 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.01
- Source
- Bacillus megaterium
- Molecule
- Bifunctional cytochrome P450/NADPH--P450 reductase
- EC
- 1.14.14.1, 1.6.2.4
- UniProt
- P14779
- Ligands
- HEM, W10
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.01 · 1 distinct chain · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 452 | 54% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- W10 · (2~{S})-3-(1~{H}-indol-3-yl)-2-[2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,10-nonadecakis(fluoranyl)decanoylamino]propanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.88 | 0.90 | 90 | HEM, W10 |
| 2 | 1185 | 0.85 | 0.85 | 119 | HEM, W10 |
| 3 | 469 | 0.63 | 0.76 | 52 | empty |
| 4 | 290 | 0.58 | 0.78 | 36 | empty |
| 5 | 271 | 0.51 | 0.74 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 907 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5B2Y · Crystal structure of P450BM3 with N-perfluorodecanoyl-L-tryptophan · 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 0.99
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 P14779
- Elsewhere: RCSB PDB 5B2Y · PDBe 5B2Y · UniProt P14779
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