Research workbench
Mycf mycinamicin III 3'-O-methyltransferase in complex with mg
Analyse Mycf mycinamicin III 3'-O-methyltransferase in complex with mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XVZ
- Type
- protein
- Length
- 799 residues
- Chains
- 4
- 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
- MG, CL
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mycinamicin III 3''-O-methyltransferase (EC 2.1.1.237) | protein | 200 | 41% helix, 18% strand | Q49492 |
| B | Mycinamicin III 3''-O-methyltransferase (EC 2.1.1.237) | protein | 197 | 42% helix, 18% strand | Q49492 |
| C | Mycinamicin III 3''-O-methyltransferase (EC 2.1.1.237) | protein | 203 | 40% helix, 18% strand | Q49492 |
| D | Mycinamicin III 3''-O-methyltransferase (EC 2.1.1.237) | protein | 199 | 41% helix, 18% strand | Q49492 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.44 | 0.82 | 28 | empty |
| 2 | 82 | 0.37 | 0.77 | 29 | CL, MG |
Interfaces
3 interfaces between chains.
- A–B · 1169 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1124 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 57 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4XVZ · MycF mycinamicin III 3'-O-methyltransferase in complex with Mg · the same entry in another collection · chain D against D, 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 B 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 Q49492
- Elsewhere: RCSB PDB 4XVZ · PDBe 4XVZ · UniProt Q49492
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