Research workbench
Crystal structure of P450BM3 with N-(3-cyclohexylpropanoyl)-L-prolyl- L-phenylalanine
Analyse Crystal structure of P450BM3 with N-(3-cyclohexylpropanoyl)-L-prolyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K3Q
- Type
- protein
- Length
- 906 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional cytochrome P450/NADPH--P450 reductase
- EC
- 1.14.14.1, 1.6.2.4
- UniProt
- P14779
- Ligands
- HEM, D0F
- Pockets
- 8 · 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 cytochrome P450/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
- D0F · (2S)-2-[[(2S)-1-(3-cyclohexylpropanoyl)pyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid · 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
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 | 1018 | 0.86 | 0.87 | 114 | HEM, DMS, D0F |
| 2 | 1007 | 0.86 | 0.87 | 113 | HEM, DMS, D0F |
| 3 | 375 | 0.57 | 0.75 | 51 | empty |
| 4 | 290 | 0.53 | 0.75 | 38 | empty |
| 5 | 161 | 0.51 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 934 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6K3Q · Crystal Structure of P450BM3 with N-(3-cyclohexylpropanoyl)-L-prolyl-L-phenylalanine · 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 A 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 6K3Q · PDBe 6K3Q · UniProt P14779
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