Research workbench
Structure of the mixed-function P450 mycg in P21 space group
Analyse Structure of the mixed-function P450 mycg in P21 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YGX
- Type
- protein
- Length
- 1,572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P-450-like protein
- UniProt
- Q59523
- Ligands
- HEM
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | P-450-like protein | protein | 393 | 52% helix, 10% strand | Q59523 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D
- SIN · Succinic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.84 | 0.84 | 96 | HEM |
| 2 | 1123 | 0.84 | 0.84 | 98 | HEM |
| 3 | 1186 | 0.84 | 0.84 | 89 | HEM |
| 4 | 1196 | 0.83 | 0.84 | 96 | HEM, GOL |
| 5 | 1055 | 0.82 | 0.84 | 96 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 698 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 649 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 262 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2YGX · Structure of the mixed-function P450 MycG 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 2YGX · PDBe 2YGX · UniProt Q59523
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