Research workbench
Crystal structure of human P450 3A4 in complex with erythromycin
Analyse Crystal structure of human P450 3A4 in complex with erythromycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J0D
- Type
- protein
- Length
- 891 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 3A4
- EC
- 1.14.14.1, 1.14.13.67, 1.14.13.97
- UniProt
- P08684
- Ligands
- HEM, ERY
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 3A4 (EC 1.14.14.1, 1.14.13.67, 1.14.13.97) | protein | 446 | 51% helix, 9% strand | P08684 |
| B | Cytochrome P450 3A4 (EC 1.14.14.1, 1.14.13.67, 1.14.13.97) | protein | 445 | 51% helix, 9% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- ERY · Erythromycin A · ligand · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.82 | 0.83 | 65 | HEM, ERY |
| 2 | 1089 | 0.79 | 0.81 | 82 | HEM |
| 3 | 196 | 0.47 | 0.74 | 27 | empty |
| 4 | 163 | 0.43 | 0.73 | 26 | empty |
| 5 | 92 | 0.36 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 2J0D · PDBe 2J0D · UniProt P08684
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