MolNFT v1 · #94323 · protein
Crystal structure of S-adenosylmethionine-dependent methyltransferase from escherichia COLI in complex with S-adenosylmethionine.
4HTF: “Crystal structure of S-adenosylmethionine-dependent methyltransferase from escherichia COLI in complex with…”. X-ray diffraction, 2 ligands (SAM, SO4), 5 pockets (best druggability 0.52). MolNFT v1 #94323 on GenesisL1: 3D structure…
- PDB
- 4HTF
- Type
- protein
- Length
- 491 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine-dependent methyltransferase
- UniProt
- Q8XDG3
- Ligands
- SAM, SO4
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine-dependent methyltransferase | protein | 244 | 47% helix, 21% strand | Q8XDG3 |
| B | S-adenosylmethionine-dependent methyltransferase | protein | 247 | 47% helix, 21% strand | Q8XDG3 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- BME · Beta-mercaptoethanol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.52 | 0.76 | 34 | SAM |
| 2 | 274 | 0.52 | 0.75 | 41 | SAM, SO4, ACT |
| 3 | 87 | 0.37 | 0.76 | 18 | empty |
| 4 | 59 | 0.32 | 0.76 | 16 | BME |
| 5 | 57 | 0.29 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1458 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified, 1 covalent (engineered, additive adduct, oxidation).
Compared structures
- 4HTF · Crystal structure of S-adenosylmethionine-dependent methyltransferase from Escherichia… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8XDG3 · AlphaFold monomer V2.0 prediction for tRNA 5-carboxymethoxyuridine methyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q8XDG3
- Elsewhere: RCSB PDB 4HTF · PDBe 4HTF · UniProt Q8XDG3
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