Research workbench
Crystal structure of sah-bound podospora anserina methyltransferase PAMTH1
Analyse Crystal structure of sah-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
- 4YMH
- Type
- protein
- Length
- 943 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative SAM-dependent O-methyltranferase
- UniProt
- Q9HGR1
- Ligands
- SAH
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative SAM-dependent O-methyltranferase | protein | 239 | 48% helix, 18% strand | Q9HGR1 |
| B, C | Putative SAM-dependent O-methyltranferase | protein | 235 | 47% helix, 19% strand | Q9HGR1 |
| D | Putative SAM-dependent O-methyltranferase | protein | 234 | 47% helix, 18% strand | Q9HGR1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.79 | 0.96 | 23 | empty |
| 2 | 121 | 0.79 | 0.97 | 23 | empty |
| 3 | 373 | 0.72 | 0.84 | 52 | SAH |
| 4 | 462 | 0.71 | 0.82 | 57 | SAH |
| 5 | 420 | 0.71 | 0.82 | 57 | SAH |
Interfaces
3 interfaces between chains.
- C–D · 3092 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 3078 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 220 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4YMH · Crystal structure of SAH-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 4YMH · PDBe 4YMH · UniProt Q9HGR1
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