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Crystal structure of udp-glucosyltransferase, UGT74F2, with udp and salicylic acid
Analyse Crystal structure of udp-glucosyltransferase, UGT74F2, with udp and salicylic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U6M
- Type
- protein
- Length
- 887 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, BGC
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glycosyltransferase 74F2 (EC 2.4.1.-) | protein | 442 | 44% helix, 13% strand | O22822 |
| B | Udp-glycosyltransferase 74F2 (EC 2.4.1.-) | protein | 445 | 44% 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
- BGC · beta-D-glucopyranose · sugar · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.82 | 0.83 | 106 | BGC, UDP, SAL |
| 2 | 1112 | 0.81 | 0.82 | 97 | BGC, UDP, SAL |
| 3 | 121 | 0.53 | 0.82 | 28 | empty |
| 4 | 184 | 0.53 | 0.78 | 26 | empty |
| 5 | 165 | 0.50 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 951 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (glycosylation).
Compared structures
- 5U6M · Crystal structure of UDP-glucosyltransferase, UGT74F2, 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 5U6M · PDBe 5U6M · UniProt O22822
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