MolNFT v1 · #140911 · protein
The crystal structure of CYP199A4 binding with 4-N-propyl benzoic acid
5YQH · Cytochrome P450: “The crystal structure of CYP199A4 binding with 4-N-propyl benzoic acid”. X-ray diffraction, 4 ligands (8ZX, HEM, SO4), 13 pockets (best druggability 0.86). MolNFT v1 #140911 on GenesisL1: 3D structure, binding…
- PDB
- 5YQH
- Type
- protein
- Length
- 1,572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450
- UniProt
- Q2IU02
- Ligands
- 8ZX, HEM, SO4, CL
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome P450 | protein | 393 | 48% helix, 14% strand | Q2IU02 |
Ligands and binding sites
- 8ZX · 4-methoxybenzamide · ligand · 8 copies · chains A, C, B, D
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 14 copies · chains A, D, B, C
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.86 | 0.94 | 57 | HEM, 8ZX |
| 2 | 373 | 0.85 | 0.94 | 60 | HEM, 8ZX |
| 3 | 365 | 0.85 | 0.94 | 60 | HEM, 8ZX, CL |
| 4 | 322 | 0.85 | 0.94 | 48 | HEM, 8ZX |
| 5 | 1157 | 0.82 | 0.83 | 120 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 1189 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 582 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 439 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 230 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5YQH · The crystal structure of CYP199A4 binding with 4-n-Propyl benzoic acid · the same entry in another collection · chain A against A, 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 Q2IU02
- Elsewhere: RCSB PDB 5YQH · PDBe 5YQH · UniProt Q2IU02
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