Research workbench
The 1.9 a crystal structure of CYP154C5 from nocardia farcinica in complex with progesterone
Analyse The 1.9 a crystal structure of CYP154C5 from nocardia farcinica in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J6C
- Type
- protein
- Length
- 813 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 monooxygenase
- UniProt
- Q5YNS8
- Ligands
- STR, HEM, MG, K
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 monooxygenase | protein | 407 | 53% helix, 10% strand | Q5YNS8 |
| B | Cytochrome P450 monooxygenase | protein | 406 | 52% helix, 10% strand | Q5YNS8 |
Ligands and binding sites
- STR · Progesterone · ligand · 2 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.86 | 0.91 | 63 | HEM, STR, K |
| 2 | 590 | 0.86 | 0.90 | 58 | STR, HEM, K |
| 3 | 241 | 0.47 | 0.74 | 27 | empty |
| 4 | 118 | 0.36 | 0.73 | 19 | empty |
| 5 | 108 | 0.35 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 149 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4J6C · The 1.9 A crystal structure of CYP154C5 from Nocardia farcinica in complex with… · 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 Q5YNS8
- Elsewhere: RCSB PDB 4J6C · PDBe 4J6C · UniProt Q5YNS8
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