MolNFT v1 · #125445 · protein
The 2.25 a crystal structure of CYP109E1 from bacillus megaterium in complex with testosterone
5L94 · Cytochrome P450: “The 2.25 a crystal structure of CYP109E1 from bacillus megaterium in complex with testosterone”. X-ray diffraction, 2 ligands (HEM, TES), 6 pockets (best druggability 0.85). MolNFT v1 #125445 on GenesisL1: 3D…
- PDB
- 5L94
- Type
- protein
- Length
- 745 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450
- EC
- 1.14.14.-
- UniProt
- D5DKI8
- Ligands
- HEM, TES
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 (EC 1.14.14.-) | protein | 385 | 54% helix, 9% strand | D5DKI8 |
| B | Cytochrome P450 (EC 1.14.14.-) | protein | 360 | 53% helix, 10% strand | D5DKI8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- TES · Testosterone · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.85 | 0.85 | 86 | HEM, TES |
| 2 | 584 | 0.75 | 0.82 | 62 | HEM |
| 3 | 909 | 0.71 | 0.76 | 67 | empty |
| 4 | 294 | 0.56 | 0.76 | 37 | empty |
| 5 | 80 | 0.34 | 0.75 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 375 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5L94 · The 2.25 A crystal structure of CYP109E1 from Bacillus megaterium 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 D5DKI8
- Elsewhere: RCSB PDB 5L94 · PDBe 5L94 · UniProt D5DKI8
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