Research workbench
Crystal structure of SAM-bound podospora anserina methyltransferase PAMTH1
Analyse Crystal structure of SAM-bound podospora anserina methyltransferase PAMTH1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YMG
- Type
- protein
- Length
- 473 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative SAM-dependent O-methyltranferase
- UniProt
- Q9HGR1
- Ligands
- SAM, MG, PO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative SAM-dependent O-methyltranferase | protein | 234 | 47% helix, 19% strand | Q9HGR1 |
| B | Putative SAM-dependent O-methyltranferase | protein | 239 | 45% helix, 19% strand | Q9HGR1 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.78 | 0.96 | 21 | empty |
| 2 | 490 | 0.73 | 0.82 | 55 | SAM, PO4 |
| 3 | 430 | 0.72 | 0.83 | 56 | SAM, PO4 |
| 4 | 147 | 0.43 | 0.76 | 20 | PG4, MG |
Interfaces
1 interface between chains.
- A–B · 3166 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 4YMG · Crystal structure of SAM-bound Podospora anserina methyltransferase PaMTH1 · 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 Q9HGR1
- Elsewhere: RCSB PDB 4YMG · PDBe 4YMG · UniProt Q9HGR1
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