MolNFT v1 · #117128 · protein
Crystal structure of ASP251GLY/GLN307HIS mutant of cytochrome P450 BM3 in complex with N-palmitoylglycine
5DYZ · Bifunctional P-450/NADPH-P450 reductase: “Crystal structure of ASP251GLY/GLN307HIS mutant of cytochrome P450 BM3 in complex with N-palmitoylglycine”. X-ray diffraction, 2 ligands (HEM, 140), 9 pockets (best druggability 0.89).…
- PDB
- 5DYZ
- Type
- protein
- Length
- 898 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, 140
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional P-450/NADPH-P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 445 | 53% helix, 11% strand | P14779 |
| C | Bifunctional P-450/NADPH-P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 453 | 53% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, C
- 140 · N-palmitoylglycine · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.89 | 0.93 | 80 | HEM |
| 2 | 662 | 0.88 | 0.92 | 78 | HEM, 140 |
| 3 | 671 | 0.67 | 0.76 | 76 | empty |
| 4 | 141 | 0.54 | 0.81 | 21 | empty |
| 5 | 145 | 0.54 | 0.81 | 24 | empty |
Interfaces
1 interface between chains.
- A–C · 994 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5DYZ · Crystal structure of Asp251Gly/Gln307His mutant of cytochrome P450 BM3 in complex with… · 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 0.98
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 5DYZ · PDBe 5DYZ · UniProt P14779
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