Research workbench
Mixed-function P450 mycg in complex with mycinamicin III in C2221 space group
Analyse Mixed-function P450 mycg in complex with mycinamicin III in C2221 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y5Z
- Type
- protein
- Length
- 1,181 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P-450-like protein
- UniProt
- Q59523
- Ligands
- HEM, ZM3, BEN
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P-450-like protein | protein | 393 | 51% helix, 10% strand | Q59523 |
| B, C | P-450-like protein | protein | 394 | 51% helix, 10% strand | Q59523 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- ZM3 · Mycinamicin III · ligand · 3 copies · chains A, B, C
- BEN · Benzamidine · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 10 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.84 | 0.85 | 98 | GOL |
| 2 | 1175 | 0.84 | 0.84 | 99 | HEM, ZM3 |
| 3 | 1185 | 0.83 | 0.84 | 99 | HEM, ZM3, GOL |
| 4 | 1162 | 0.83 | 0.84 | 95 | HEM, ZM3 |
| 5 | 355 | 0.60 | 0.77 | 40 | empty |
Interfaces
2 interfaces between chains.
- A–C · 611 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 392 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2Y5Z · Mixed-function P450 MycG in complex with mycinamicin III in C2221 space group · the same entry in another collection · chain C against C, TM-score 1.00
- Q59523 · AlphaFold monomer V2.0 prediction for mycinamicin IV HYDROXYLASE/EPOXIDASE (Q59523) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q59523
- Elsewhere: RCSB PDB 2Y5Z · PDBe 2Y5Z · UniProt Q59523
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.