Research workbench
Crystal structure of udp-glucosyltransferase, UGT74F2 (T15S), with udp and 2-bromobenzoic 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
- 5V2J
- Type
- protein
- Length
- 888 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, 7WV, BGC
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-glycosyltransferase 74F2 (EC 2.4.1.-) | protein | 444 | 46% helix, 13% strand | O22822 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- 7WV · 2-bromobenzoic acid · ligand · 2 copies · chains A, B
- 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.79 | 0.84 | 72 | BGC, UDP, 7WV |
| 2 | 742 | 0.79 | 0.83 | 71 | BGC, UDP, 7WV |
| 3 | 359 | 0.69 | 0.82 | 57 | empty |
| 4 | 594 | 0.69 | 0.78 | 71 | BGC |
| 5 | 106 | 0.50 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 696 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (glycosylation).
Compared structures
- 5V2J · Crystal structure of UDP-glucosyltransferase, UGT74F2 (T15S), with UDP and 2-bromobenzoic… · 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 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 O22822
- Elsewhere: RCSB PDB 5V2J · PDBe 5V2J · UniProt O22822
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