MolNFT v1 · #95979 · protein
The 2.4 a crystal structure of CYP154C5 from nocardia farcinica in complex with testosterone
4J6D · Cytochrome P450 monooxygenase: “The 2.4 a crystal structure of CYP154C5 from nocardia farcinica in complex with testosterone”. X-ray diffraction, 4 ligands (HEM, TES, MG), 8 pockets (best druggability 0.86). MolNFT v1 #95979 on…
- PDB
- 4J6D
- Type
- protein
- Length
- 812 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 monooxygenase
- UniProt
- Q5YNS8
- Ligands
- HEM, TES, MG, K
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 monooxygenase | protein | 406 | 52% helix, 10% strand | Q5YNS8 |
| B | Cytochrome P450 monooxygenase | protein | 406 | 52% helix, 10% strand | Q5YNS8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- TES · Testosterone · 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.86 | 0.91 | 61 | HEM, TES, K |
| 2 | 535 | 0.85 | 0.91 | 58 | HEM, TES |
| 3 | 243 | 0.51 | 0.75 | 27 | empty |
| 4 | 57 | 0.38 | 0.80 | 18 | empty |
| 5 | 114 | 0.36 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 245 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4J6D · The 2.4 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 4J6D · PDBe 4J6D · UniProt Q5YNS8
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