Research workbench
Structure of CYP119 with T213A and C317H mutations
Analyse Structure of CYP119 with T213A and C317H mutations in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BV5
- Type
- protein
- Length
- 1,241 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 119
- Ligands
- HEM, PIM, PO4
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 119 | protein | 315 | 54% helix, 15% strand | — |
| B | Cytochrome P450 119 | protein | 288 | 51% helix, 15% strand | — |
| D | Cytochrome P450 119 | protein | 327 | 54% helix, 13% strand | — |
| C | Cytochrome P450 119 | protein | 311 | 54% helix, 14% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, D, C
- PIM · 4-phenyl-1H-imidazole · ligand · 3 copies · chains B, D, C
- PO4 · Phosphate ion · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.86 | 0.89 | 69 | PO4 |
| 2 | 731 | 0.83 | 0.87 | 62 | PO4 |
| 3 | 462 | 0.66 | 0.78 | 40 | HEM, PIM |
| 4 | 478 | 0.65 | 0.77 | 44 | HEM, PIM |
| 5 | 112 | 0.63 | 0.88 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1253 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1111 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 585 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5BV5 · Structure of CYP119 with T213A and C317H mutations · 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
- Elsewhere: RCSB PDB 5BV5 · PDBe 5BV5
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