MolNFT v1 · #125443 · protein
The 2.1 a crystal structure of CYP109E1 from bacillus megaterium in complex with corticosterone
5L92 · Cytochrome P450: “The 2.1 a crystal structure of CYP109E1 from bacillus megaterium in complex with corticosterone”. X-ray diffraction, 2 ligands (HEM, C0R), 5 pockets (best druggability 0.84). MolNFT v1 #125443 on GenesisL1: 3D…
- PDB
- 5L92
- Type
- protein
- Length
- 756 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, C0R
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 (EC 1.14.14.-) | protein | 386 | 53% helix, 9% strand | D5DKI8 |
| B | Cytochrome P450 (EC 1.14.14.-) | protein | 370 | 52% helix, 10% strand | D5DKI8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- C0R · Corticosterone · ligand · chains A
- MLA · Malonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.84 | 0.84 | 89 | HEM, C0R, MLA |
| 2 | 973 | 0.81 | 0.82 | 77 | empty |
| 3 | 523 | 0.75 | 0.83 | 61 | HEM |
| 4 | 73 | 0.48 | 0.83 | 16 | empty |
| 5 | 102 | 0.37 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 672 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5L92 · The 2.1 A crystal structure of CYP109E1 from Bacillus megaterium in complex with… · the same entry in another collection · chain B against B, 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 5L92 · PDBe 5L92 · UniProt D5DKI8
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