Research workbench
Myce methyltransferase from the mycinamycin biosynthetic pathway in complex with mg, sah, and mycinamycin VI
Analyse Myce methyltransferase from the mycinamycin biosynthetic pathway in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SSN
- Type
- protein
- Length
- 1,495 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase
- EC
- 2.1.1.-
- UniProt
- Q83WF2
- Ligands
- SAH, MVI, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase (EC 2.1.1.-) | protein | 386 | 40% helix, 22% strand | Q83WF2 |
| B | Methyltransferase (EC 2.1.1.-) | protein | 350 | 41% helix, 23% strand | Q83WF2 |
| C | Methyltransferase (EC 2.1.1.-) | protein | 366 | 39% helix, 23% strand | Q83WF2 |
| D | Methyltransferase (EC 2.1.1.-) | protein | 393 | 40% helix, 21% strand | Q83WF2 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, D, B, C
- MVI · Mycinamicin VI · ligand · 2 copies · chains A, C, D, B
- MG · Magnesium ion · metal · 3 copies · chains A, C, D
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, D, C
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.86 | 0.89 | 110 | DMS |
| 2 | 666 | 0.83 | 0.87 | 78 | empty |
| 3 | 514 | 0.82 | 0.89 | 66 | empty |
| 4 | 622 | 0.79 | 0.84 | 57 | MG, SAH, MVI |
| 5 | 625 | 0.79 | 0.84 | 51 | MG, SAH, MVI |
Interfaces
6 interfaces between chains.
- A–D · 2852 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2287 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2194 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1954 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1775 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3SSN · MycE Methyltransferase from the Mycinamycin Biosynthetic Pathway in Complex with Mg, SAH… · the same entry in another collection · chain D against D, TM-score 1.00
- Q83WF2 · AlphaFold monomer V2.0 prediction for mycinamicin VI 2''-O-methyltransferase (Q83WF2) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q83WF2
- Elsewhere: RCSB PDB 3SSN · PDBe 3SSN · UniProt Q83WF2
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