MolNFT v1 · #137056 · protein
Crystal structure of the cysteine depleted CYP3A4 bound to bromoergocryptine
5VCG · Cytochrome P450 3A4: “Crystal structure of the cysteine depleted CYP3A4 bound to bromoergocryptine”. X-ray diffraction, 2 ligands (HEM, 08Y), 4 pockets (best druggability 0.87). MolNFT v1 #137056 on GenesisL1: 3D structure, binding…
- PDB
- 5VCG
- Type
- protein
- Length
- 461 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 3A4
- EC
- 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.9
- UniProt
- P08684
- Ligands
- HEM, 08Y
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 3A4 (EC 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.9) | protein | 461 | 51% helix, 10% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- 08Y · bromoergocryptine · ligand · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.87 | 0.87 | 77 | HEM, 08Y |
| 2 | 139 | 0.49 | 0.79 | 22 | empty |
| 3 | 236 | 0.49 | 0.74 | 33 | empty |
| 4 | 121 | 0.47 | 0.78 | 29 | GOL |
Compared structures
- 5VCG · Crystal structure of the cysteine depleted CYP3A4 bound to bromoergocryptine · the same entry in another collection · chain A against A, TM-score 1.00
- P08684 · AlphaFold monomer V2.0 prediction for cytochrome P450 3A4 (P08684) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P08684
- Elsewhere: RCSB PDB 5VCG · PDBe 5VCG · UniProt P08684
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