Research workbench
Human cytochrome P450 (cyp) 3A5 ternary complex with azamulin
Analyse Human cytochrome P450 (cyp) 3A5 ternary complex with azamulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SV2
- Type
- protein
- Length
- 1,824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 3A5
- EC
- 1.14.14.1
- UniProt
- P20815
- Ligands
- MWY, HEM
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 465 | 52% helix, 9% strand | P20815 |
| B | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 465 | 51% helix, 9% strand | P20815 |
| C | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 456 | 53% helix, 9% strand | P20815 |
| D | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 438 | 52% helix, 10% strand | P20815 |
Ligands and binding sites
- MWY · (3as,4r,5s,6r,8r,9r,9ar,10r)-6-ethyl-5-hydroxy-4,6,9, 10-tetramethyl-1-oxodecahydro-3A,9-propanocyclopenta[8]annulen-8-yl [(5-amino-1H-1,2,4-triazol-3-yl)sulfanyl]acetate · ligand · 8 copies · chains A, B, C, D
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.85 | 0.86 | 86 | HEM, MWY |
| 2 | 1104 | 0.85 | 0.86 | 77 | HEM, MWY |
| 3 | 1169 | 0.85 | 0.86 | 83 | HEM, MWY |
| 4 | 1144 | 0.85 | 0.85 | 77 | HEM, MWY |
| 5 | 769 | 0.81 | 0.84 | 82 | empty |
Interfaces
5 interfaces between chains.
- C–D · 893 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 781 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 730 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 416 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 160 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 P20815
- Elsewhere: RCSB PDB 7SV2 · PDBe 7SV2 · UniProt P20815
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