MolNFT v1 · #102592 · protein
Crystal structure of the TYLM1 N,N-dimethyltransferase in complex with sah and tdp-QUI3NME2
4OQD · 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-QUI3NME2”. X-ray diffraction, 2 ligands (SAH, QDM), 5 pockets (best druggability 0.80). MolNFT…
- PDB
- 4OQD
- Type
- protein
- Length
- 960 residues
- Chains
- 4
- 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, QDM
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 31% 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, 37% strand | P95748 |
| B, D | Dtdp-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N- dimethyltransferase (EC 2.1.1.235) | protein | 240 | 31% helix, 36% strand | P95748 |
| C | Dtdp-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N- dimethyltransferase (EC 2.1.1.235) | protein | 241 | 30% helix, 37% strand | P95748 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- QDM · TDP-3,6-dideoxy-3-N,N-dimethylglucose · ligand · 4 copies · chains A, B, C, D
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 | 1093 | 0.80 | 0.81 | 106 | SAH, QDM |
| 2 | 862 | 0.80 | 0.83 | 92 | SAH, QDM |
| 3 | 614 | 0.79 | 0.84 | 75 | SAH, QDM |
| 4 | 462 | 0.76 | 0.84 | 60 | SAH, QDM |
| 5 | 72 | 0.35 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- C–D · 804 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 788 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 558 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 287 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4OQD · Crystal structure of the tylM1 N,N-dimethyltransferase in complex with SAH and… · 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 4OQD · PDBe 4OQD · UniProt P95748
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