Research workbench
Human cytochrome P450 3A5 (CYP3A5)
Analyse Human cytochrome P450 3A5 (CYP3A5) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VEU
- Type
- protein
- Length
- 5,487 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 3A5
- EC
- 1.14.14.1
- UniProt
- P20815
- Ligands
- HEM, RIT
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 10 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 462 | 53% helix, 9% strand | P20815 |
| B, J | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 458 | 53% helix, 9% strand | P20815 |
| C | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 469 | 52% helix, 9% strand | P20815 |
| D, H | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 459 | 52% helix, 9% strand | P20815 |
| E | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 441 | 53% helix, 8% strand | P20815 |
| F | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 456 | 53% helix, 9% strand | P20815 |
| G | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 455 | 52% helix, 9% strand | P20815 |
| I | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 464 | 52% helix, 9% strand | P20815 |
| K | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 458 | 53% helix, 9% strand | P20815 |
| L | Cytochrome P450 3A5 (EC 1.14.14.1) | protein | 448 | 54% helix, 9% strand | P20815 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- RIT · Ritonavir · ligand · 3 copies · chains A, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.87 | 0.87 | 93 | HEM, RIT |
| 2 | 1010 | 0.87 | 0.87 | 65 | HEM |
| 3 | 1029 | 0.87 | 0.87 | 69 | HEM, RIT |
| 4 | 1081 | 0.86 | 0.87 | 67 | HEM, RIT |
| 5 | 1041 | 0.86 | 0.87 | 71 | HEM |
Interfaces
23 interfaces between chains.
- A–C · 700 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 620 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 563 Ų buried · 3 hydrogen bonds · protein-protein
- G–J · 555 Ų buried · 3 hydrogen bonds · protein-protein
- B–L · 528 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VEU · Human Cytochrome P450 3A5 (CYP3A5) · the same entry in another collection · chain L against L, 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
- Every structure of UniProt P20815
- Elsewhere: RCSB PDB 5VEU · PDBe 5VEU · UniProt P20815
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