Research workbench
Structure of the mixed-function P450 mycg in complex with mycinamicin V in P21 space group
Analyse Structure of the mixed-function P450 mycg in complex with mycinamicin V in P21… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y5N
- Type
- protein
- Length
- 794 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P-450-like protein
- UniProt
- Q59523
- Ligands
- HEM, MYV, MG
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P-450-like protein | protein | 394 | 51% helix, 10% strand | Q59523 |
| B | P-450-like protein | protein | 400 | 50% helix, 10% strand | Q59523 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- MYV · Mycinamicin V · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal
- GOL · Glycerol · additive · 13 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.84 | 0.85 | 94 | HEM, MYV, GOL |
| 2 | 1180 | 0.83 | 0.84 | 96 | HEM, MYV |
| 3 | 184 | 0.48 | 0.76 | 38 | empty |
| 4 | 176 | 0.42 | 0.73 | 24 | GOL |
| 5 | 79 | 0.41 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 340 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2Y5N · Structure of the mixed-function P450 MycG in complex with mycinamicin V in P21 space group · the same entry in another collection · chain A against A, 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 2Y5N · PDBe 2Y5N · UniProt Q59523
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