Research workbench
Mycf mycinamicin III 3'-O-methyltransferase (E35Q, E139A variant) in complex with mg, sah and mycinamicin VI (myce substrate)
Analyse Mycf mycinamicin III 3'-O-methyltransferase (E35Q, E139A variant) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X7W
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mycinamicin III 3''-O-methyltransferase
- EC
- 2.1.1.237
- UniProt
- Q49492
- Ligands
- SAH, MVI, MG
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mycinamicin III 3''-O-methyltransferase (EC 2.1.1.237) | protein | 250 | 40% helix, 16% strand | Q49492 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- MVI · Mycinamicin VI · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.75 | 0.83 | 61 | SAH, MVI |
| 2 | 451 | 0.75 | 0.84 | 64 | SAH, MG, MVI |
Interfaces
1 interface between chains.
- A–B · 1089 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4X7W · MycF mycinamicin III 3'-O-methyltransferase (E35Q, E139A variant) in complex with Mg, SAH… · the same entry in another collection · chain B against B, TM-score 1.00
- Q49492 · AlphaFold monomer V2.0 prediction for mycinamicin III 3''-O-methyltransferase (Q49492) · a predicted model of the same protein · chain A against A, 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 Q49492
- Elsewhere: RCSB PDB 4X7W · PDBe 4X7W · UniProt Q49492
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