Research workbench
Crystal structure of cytochrome P450DA mutant (N190F/V356L/A486E) heme domain
Analyse Crystal structure of cytochrome P450DA mutant (N190F/V356L/A486E) heme domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F3W
- Type
- protein
- Length
- 1,818 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450
- Ligands
- HEM, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 | protein | 464 | 49% helix, 10% strand | — |
| B | Cytochrome P450 | protein | 460 | 50% helix, 10% strand | — |
| C | Cytochrome P450 | protein | 454 | 51% helix, 11% strand | — |
| D | Cytochrome P450 | protein | 440 | 50% helix, 11% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.85 | 0.85 | 100 | HEM, SO4 |
| 2 | 939 | 0.84 | 0.85 | 81 | HEM |
| 3 | 837 | 0.83 | 0.85 | 76 | HEM |
| 4 | 874 | 0.83 | 0.85 | 80 | HEM |
| 5 | 711 | 0.71 | 0.78 | 59 | SO4 |
Interfaces
4 interfaces between chains.
- B–C · 1368 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1353 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 801 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 792 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (heme attachment).
Compared structures
- 7F3W · Crystal structure of cytochrome P450DA mutant (N190F/V356L/A486E) heme domain · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7F3W · PDBe 7F3W
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