MolNFT v1 · #89598 · protein
Cytochrome P450 BM3H-B7 mri sensor bound to dopamine
4DU2 · Cytochrome P450 BM3 variant B7: “Cytochrome P450 BM3H-B7 mri sensor bound to dopamine”. X-ray diffraction, 2 ligands (HEM, LDP), 12 pockets (best druggability 0.86). MolNFT v1 #89598 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4DU2
- Type
- protein
- Length
- 887 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 BM3 variant B7
- EC
- 1.14.14.1
- UniProt
- P14779
- Ligands
- HEM, LDP
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Cytochrome P450 BM3 variant B7 (EC 1.14.14.1) | protein | 444 | 55% helix, 11% strand | P14779 |
| A | Cytochrome P450 BM3 variant B7 (EC 1.14.14.1) | protein | 443 | 54% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, A
- LDP · L-dopamine · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.86 | 0.90 | 82 | HEM, LDP |
| 2 | 810 | 0.84 | 0.87 | 92 | HEM, LDP |
| 3 | 224 | 0.54 | 0.78 | 28 | empty |
| 4 | 186 | 0.52 | 0.78 | 27 | empty |
| 5 | 301 | 0.52 | 0.74 | 40 | empty |
Interfaces
1 interface between chains.
- B–A · 892 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4DU2 · cytochrome P450 BM3h-B7 MRI sensor bound to dopamine · 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 4DU2 · PDBe 4DU2 · UniProt P14779
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