MolNFT v1 · #79074 · protein
Myce methyltransferase from the mycinamycin biosynthetic pathway in complex with mg, sah, and mycinamycin VI
3SSN: “Myce methyltransferase from the mycinamycin biosynthetic pathway in complex with mg, sah, and mycinamycin VI”. X-ray diffraction, 3 ligands (SAH, MVI, MG), 20 pockets (best druggability 0.86). MolNFT v1 #79074 on GenesisL1: 3D…
- 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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