Research workbench
X-ray crystal structure the N,N-dimethyltransferase TYLM1 from streptomyces fradiae in complex with SAM and dtdp-phenol
Analyse X-ray crystal structure the N,N-dimethyltransferase TYLM1 from streptomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PFG
- Type
- protein
- Length
- 241 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-methyltransferase
- UniProt
- P95748
- Ligands
- SAM, TLO
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-methyltransferase | protein | 241 | 30% helix, 37% strand | P95748 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- TLO · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phenoxy) phosphoryl]oxy}phosphoryl]thymidine · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.75 | 0.84 | 57 | SAM, EDO, TLO |
Compared structures
- 3PFG · X-Ray crystal structure the N,N-dimethyltransferase TylM1 from Streptomyces fradiae in… · the same entry in another collection · chain A against A, TM-score 1.00
- P95748 · AlphaFold monomer V2.0 prediction for dtdp-3-amino-3,6-dideoxy-alpha- D-glucopyranose… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P95748
- Elsewhere: RCSB PDB 3PFG · PDBe 3PFG · UniProt P95748
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