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Crystal structure of udp-glucosyltransferase, UGT74F2 (T15S), with udp and salicylic acid
Analyse Crystal structure of udp-glucosyltransferase, UGT74F2 (T15S), with udp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U6N
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glycosyltransferase 74F2
- EC
- 2.4.1.-
- UniProt
- O22822
- Ligands
- UDP, SAL, GLN, BGC
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glycosyltransferase 74F2 (EC 2.4.1.-) | protein | 442 | 47% helix, 14% strand | O22822 |
| B | Udp-glycosyltransferase 74F2 (EC 2.4.1.-) | protein | 448 | 45% helix, 13% strand | O22822 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- SAL · 2-hydroxybenzoic acid · ligand · 2 copies · chains A, B
- GLN · Glutamine · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.83 | 0.84 | 106 | BGC, UDP, SAL |
| 2 | 808 | 0.82 | 0.84 | 96 | BGC, UDP, SAL |
| 3 | 90 | 0.51 | 0.83 | 16 | empty |
| 4 | 128 | 0.49 | 0.79 | 22 | empty |
| 5 | 101 | 0.48 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 977 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 1 covalent (glycosylation, covalent ligand).
Compared structures
- 5U6N · Crystal structure of UDP-glucosyltransferase, UGT74F2 (T15S), with UDP and salicylic acid · the same entry in another collection · chain A against A, TM-score 1.00
- O22822 · AlphaFold monomer V2.0 prediction for udp-glycosyltransferase 74F2 (O22822) · a predicted model of the same protein · chain B 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 O22822
- Elsewhere: RCSB PDB 5U6N · PDBe 5U6N · UniProt O22822
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