Research workbench
The crystal structure of P450 CYP121 in complex with lead compound 7B
Analyse The crystal structure of P450 CYP121 in complex with lead compound 7B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OPA
- Type
- protein
- Length
- 393 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mycocyclosin synthase
- EC
- 1.14.21.9
- UniProt
- P9WPP6
- Ligands
- HEM, A2W, SO4
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mycocyclosin synthase (EC 1.14.21.9) | protein | 393 | 52% helix, 10% strand | P9WPP6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- A2W · 3-(4-fluorophenyl)-4-(imidazol-1-ylmethyl)-1-phenyl-pyrazole · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.87 | 0.89 | 76 | HEM, A2W, SO4 |
| 2 | 50 | 0.39 | 0.81 | 18 | empty |
| 3 | 59 | 0.37 | 0.79 | 19 | empty |
Compared structures
- 5OPA · The crystal structure of P450 CYP121 in complex with lead compound 7b · the same entry in another collection · chain A against A, TM-score 1.00
- P9WPP6 · AlphaFold monomer V2.0 prediction for mycocyclosin synthase (P9WPP6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P9WPP6
- Elsewhere: RCSB PDB 5OPA · PDBe 5OPA · UniProt P9WPP6
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