Research workbench
Crystal structure of cytochrome P450DA heme domain
Analyse Crystal structure of cytochrome P450DA heme domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F3H
- Type
- protein
- Length
- 1,830 residues
- Chains
- 4
- 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
- Ligands
- HEM, SER, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 462 | 52% helix, 10% strand | — |
| B | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 455 | 51% helix, 11% strand | — |
| C | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 449 | 49% helix, 11% strand | — |
| D | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 464 | 50% helix, 10% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- SER · Serine · ligand · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.84 | 0.86 | 71 | HEM |
| 2 | 1124 | 0.83 | 0.83 | 94 | HEM |
| 3 | 910 | 0.82 | 0.84 | 80 | HEM |
| 4 | 812 | 0.81 | 0.84 | 69 | HEM |
| 5 | 500 | 0.71 | 0.80 | 49 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1412 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1283 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 806 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 788 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7F3H · Crystal structure of cytochrome P450DA 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 7F3H · PDBe 7F3H
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