MolNFT v1 · #156314 · protein
Structure of phytolacca americana UGT3 with 18-crown-6
6LZY · Glycosyltransferase: “Structure of phytolacca americana UGT3 with 18-crown-6”. X-ray diffraction, 3 ligands (O4B, NA, BR), 10 pockets (best druggability 0.86). MolNFT v1 #156314 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6LZY
- Type
- protein
- Length
- 907 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase
- EC
- 2.4.1.-
- UniProt
- B5MGN9
- Ligands
- O4B, NA, BR
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyltransferase (EC 2.4.1.-) | protein | 454 | 48% helix, 14% strand | B5MGN9 |
| B | Glycosyltransferase (EC 2.4.1.-) | protein | 453 | 47% helix, 14% strand | B5MGN9 |
Ligands and binding sites
- O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · chains A, B
- NA · Sodium ion · metal · chains A, B
- BR · Bromide ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.86 | 0.87 | 111 | EDO |
| 2 | 996 | 0.84 | 0.85 | 90 | EDO |
| 3 | 755 | 0.80 | 0.84 | 76 | EDO, NA, O4B |
| 4 | 84 | 0.66 | 0.92 | 24 | empty |
| 5 | 89 | 0.46 | 0.80 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 582 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6LZY · Structure of Phytolacca americana UGT3 with 18-crown-6 · 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 B5MGN9
- Elsewhere: RCSB PDB 6LZY · PDBe 6LZY · UniProt B5MGN9
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