MolNFT v1 · #102593 · protein
Crystal structure of the TYLM1 N,N-dimethyltransferase in complex with sah and tdp-FUC3NME
4OQE · Dtdp-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N…: “Crystal structure of the TYLM1 N,N-dimethyltransferase in complex with sah and tdp-FUC3NME”. X-ray diffraction, 2 ligands (SAH, MMF), 3 pockets (best druggability 0.78). MolNFT…
- PDB
- 4OQE
- Type
- protein
- Length
- 479 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N- dimethyltransferase
- EC
- 2.1.1.235
- UniProt
- P95748
- Ligands
- SAH, MMF
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 37% 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 | 239 | 31% helix, 36% strand | P95748 |
| B | Dtdp-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N- dimethyltransferase (EC 2.1.1.235) | protein | 240 | 33% helix, 37% strand | P95748 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- MMF · dTDP-3-N-methylamino-3,6-dideoxygalactose · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.78 | 0.85 | 58 | SAH, MMF |
| 2 | 457 | 0.76 | 0.85 | 61 | SAH, MMF |
| 3 | 61 | 0.33 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 808 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4OQE · Crystal structure of the tylM1 N,N-dimethyltransferase in complex with SAH and TDP-Fuc3NMe · 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 4OQE · PDBe 4OQE · UniProt P95748
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