MolNFT v1 · #15377 · protein
Crystal structure analysis of TM0872, a putative SAM- dependent methyltransferase, complexed with SAM
1N2X · S-adenosyl-methyltransferase mraw: “Crystal structure analysis of TM0872, a putative SAM- dependent methyltransferase, complexed with SAM”. X-ray diffraction, 2 ligands (SAM, SO4), 5 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 1N2X
- Type
- protein
- Length
- 565 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosyl-methyltransferase mraw
- EC
- 2.1.1.-
- UniProt
- Q9WZX6
- Ligands
- SAM, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosyl-methyltransferase mraw (EC 2.1.1.-) | protein | 287 | 48% helix, 16% strand | Q9WZX6 |
| B | S-adenosyl-methyltransferase mraw (EC 2.1.1.-) | protein | 278 | 44% helix, 14% strand | Q9WZX6 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.73 | 0.88 | 39 | SAM |
| 2 | 273 | 0.72 | 0.86 | 44 | SAM |
| 3 | 333 | 0.67 | 0.81 | 26 | empty |
| 4 | 364 | 0.63 | 0.78 | 29 | empty |
| 5 | 50 | 0.32 | 0.77 | 14 | SO4 |
Modifications
Observed in the structure: 8 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 1N2X · Crystal Structure Analysis of TM0872, a Putative SAM-dependent Methyltransferase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WZX6 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase H… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9WZX6
- Elsewhere: RCSB PDB 1N2X · PDBe 1N2X · UniProt Q9WZX6
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