MolNFT v1 · #105888 · protein
Landomycin glycosyltransferase LANGT2, carbasugar substrate complex
4RIF · Glycosyl transferase homolog: “Landomycin glycosyltransferase LANGT2, carbasugar substrate complex”. X-ray diffraction, 1 ligand (3R2), 7 pockets (best druggability 0.81). MolNFT v1 #105888 on GenesisL1: 3D structure, binding sites…
- PDB
- 4RIF
- Type
- protein
- Length
- 749 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl transferase homolog
- UniProt
- Q9ZGC0
- Ligands
- 3R2
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl transferase homolog | protein | 370 | 48% helix, 15% strand | Q9ZGC0 |
| B | Glycosyl transferase homolog | protein | 379 | 49% helix, 15% strand | Q9ZGC0 |
Ligands and binding sites
- 3R2 · 2'-deoxy-5'-O-[(R)-{[(R)-{[(1S,3R,4R,5S)-3,4-dihydroxy-5-methylcyclohexyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-3,4-dihydrothymidine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.81 | 0.87 | 75 | 3R2 |
| 2 | 683 | 0.80 | 0.84 | 73 | 3R2 |
| 3 | 138 | 0.57 | 0.83 | 31 | empty |
| 4 | 128 | 0.53 | 0.82 | 26 | empty |
| 5 | 79 | 0.50 | 0.83 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1535 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4RIF · Landomycin Glycosyltransferase LanGT2, carbasugar substrate complex · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9ZGC0
- Elsewhere: RCSB PDB 4RIF · PDBe 4RIF · UniProt Q9ZGC0
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