MolNFT v1 · #156559 · protein
Crystal structure of TYLM1 Y14F bound to sah and dtdp-phenol
6M81 · Dtdp-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N…: “Crystal structure of TYLM1 Y14F bound to sah and dtdp-phenol”. X-ray diffraction, 2 ligands (SAH, TLO), 5 pockets (best druggability 0.82). MolNFT v1 #156559 on GenesisL1: 3D…
- PDB
- 6M81
- Type
- protein
- Length
- 953 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, TLO
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 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 | 238 | 32% helix, 37% strand | P95748 |
| C | Dtdp-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N- dimethyltransferase (EC 2.1.1.235) | protein | 237 | 33% helix, 37% strand | P95748 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- TLO · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phenoxy) phosphoryl]oxy}phosphoryl]thymidine · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.82 | 0.83 | 97 | SAH, TLO |
| 2 | 575 | 0.82 | 0.88 | 62 | SAH, TLO |
| 3 | 497 | 0.78 | 0.85 | 63 | SAH, TLO |
| 4 | 581 | 0.77 | 0.83 | 65 | SAH, TLO |
| 5 | 114 | 0.53 | 0.82 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–C · 322 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 160 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 114 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6M81 · Crystal structure of TylM1 Y14F bound to SAH and dTDP-phenol · the same entry in another collection · chain D against D, 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 C 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 6M81 · PDBe 6M81 · UniProt P95748
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