Research workbench
Structure of the alpha-N-methyltransferase (sonm) and ripp precursor (sona) heteromeric complex (with sah)
Analyse Structure of the alpha-N-methyltransferase (sonm) and ripp precursor (sona)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LTE
- Type
- protein
- Length
- 661 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tp-methylase family protein; Liga domain-containing protein
- UniProt
- Q8EGW3, Q8EGW2
- Ligands
- SAH
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tp-methylase family protein | protein | 262 | 37% helix, 21% strand | Q8EGW3 |
| B | Liga domain-containing protein | protein | 69 | 58% helix, 1% strand | Q8EGW2 |
| D | Liga domain-containing protein | protein | 68 | 62% helix, 1% strand | Q8EGW2 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.79 | 0.98 | 25 | SAH |
| 2 | 107 | 0.77 | 0.97 | 25 | SAH |
| 3 | 247 | 0.64 | 0.82 | 38 | empty |
| 4 | 240 | 0.64 | 0.82 | 33 | empty |
| 5 | 272 | 0.58 | 0.78 | 38 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2847 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 1705 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1682 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 524 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 497 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 7LTE · Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA) heteromeric… · the same entry in another collection · 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 Q8EGW3
- Every structure of UniProt Q8EGW2
- Elsewhere: RCSB PDB 7LTE · PDBe 7LTE · UniProt Q8EGW3 · UniProt Q8EGW2
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