Research workbench
Crystal structure of TylM1 Y14paF bound to SAH and dTDP-phenol
Analyse Crystal structure of TylM1 Y14paF bound to SAH and dTDP-phenol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M82
- Type
- protein
- Length
- 237 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.3971
- Source
- Streptomyces fradiae
- Molecule
- dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
- EC
- 2.1.1.235
- UniProt
- P95748
- Ligands
- SAH, TLO
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.3971 · 1 distinct chain · 31% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase (EC 2.1.1.235) | protein | 237 | 31% helix, 38% strand | P95748 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · 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 | 491 | 0.77 | 0.85 | 57 | SAH, TLO |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6M82 · Crystal structure of TYLM1 Y14PAF bound to sah and dtdp-phenol · 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 0.99
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 P95748
- Elsewhere: RCSB PDB 6M82 · PDBe 6M82 · UniProt P95748
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