Research workbench
Crystal structure of UGT85B1 from sorghum bicolor in complex with udp and P-hydroxymandelonitrile
Analyse Crystal structure of UGT85B1 from sorghum bicolor in complex 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
- 7ZF0
- Type
- protein
- Length
- 474 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyanohydrin beta-glucosyltransferase
- EC
- 2.4.1.85
- UniProt
- Q9SBL1
- Ligands
- UDP, DHR
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyanohydrin beta-glucosyltransferase (EC 2.4.1.85) | protein | 474 | 49% helix, 13% strand | Q9SBL1 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- DHR · (2S)-hydroxy(4-hydroxyphenyl)ethanenitrile · ligand · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.81 | 0.87 | 60 | UDP, EDO, DHR |
| 2 | 75 | 0.63 | 0.91 | 20 | EDO |
| 3 | 142 | 0.43 | 0.76 | 27 | empty |
| 4 | 69 | 0.35 | 0.77 | 20 | empty |
| 5 | 52 | 0.25 | 0.73 | 11 | EDO |
Compared structures
- 7ZF0 · Crystal structure of UGT85B1 from Sorghum bicolor in complex with UDP and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SBL1 · AlphaFold monomer V2.0 prediction for cyanohydrin beta- glucosyltransferase (Q9SBL1) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9SBL1
- Elsewhere: RCSB PDB 7ZF0 · PDBe 7ZF0 · UniProt Q9SBL1
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