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Crystal structure of phytolacca americana UGT3 with capsaicin and udp- 2FLUOROGLUCOSE
Analyse Crystal structure of phytolacca americana UGT3 with capsaicin and udp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VEK
- Type
- protein
- Length
- 903 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase
- EC
- 2.4.1.-
- UniProt
- B5MGN9
- Ligands
- U2F, O4B, 4DY, K
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyltransferase (EC 2.4.1.-) | protein | 452 | 45% helix, 14% strand | B5MGN9 |
| B | Glycosyltransferase (EC 2.4.1.-) | protein | 451 | 45% helix, 14% strand | B5MGN9 |
Ligands and binding sites
- U2F · Uridine-5'-diphosphate-2-deoxy-2-fluoro-alpha-D-glucose · ligand · 2 copies · chains A, B
- O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · chains A, B
- 4DY · (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide · ligand · chains B
- K · Potassium ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.86 | 0.87 | 113 | U2F |
| 2 | 1095 | 0.86 | 0.87 | 96 | 4DY, U2F |
| 3 | 1032 | 0.81 | 0.82 | 90 | O4B, K |
| 4 | 59 | 0.39 | 0.81 | 14 | empty |
| 5 | 77 | 0.39 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 562 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7VEK · Crystal structure of Phytolacca americana UGT3 with capsaicin and UDP-2fluoroglucose · 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 7VEK · PDBe 7VEK · UniProt B5MGN9
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