Research workbench
Crystal structure of P450BM3 with N-perfluorononanoyl-L-tryptophan
Analyse Crystal structure of P450BM3 with N-perfluorononanoyl-L-tryptophan in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WSP
- Type
- protein
- Length
- 906 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional P-450/NADPH-P450 reductase
- EC
- 1.14.14.1, 1.6.2.4
- UniProt
- P14779
- Ligands
- HEM, W09
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bifunctional P-450/NADPH-P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 453 | 55% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- W09 · N-(2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,9-heptadecafluorononanoyl)-L-tryptophan · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.86 | 0.87 | 116 | HEM, W09, DMS |
| 2 | 1193 | 0.85 | 0.86 | 116 | HEM, W09, DMS |
| 3 | 260 | 0.54 | 0.76 | 35 | empty |
| 4 | 182 | 0.52 | 0.78 | 23 | empty |
| 5 | 213 | 0.52 | 0.77 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 952 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3WSP · Crystal Structure of P450BM3 with N-perfluorononanoyl-L-tryptophan · the same entry in another collection · chain B against B, 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 3WSP · PDBe 3WSP · UniProt P14779
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