Research workbench
The structure of C100A mutant of Arabidopsis thaliana UDP-apiose/UDP-xylose synthase in complex with NADH and UDP-D-glucuronic acid
Analyse The structure of C100A mutant of Arabidopsis thaliana UDP-apiose/UDP-xylose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H0P
- Type
- protein
- Length
- 742 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.47
- Source
- Arabidopsis thaliana
- Molecule
- UDP-D-apiose/UDP-D-xylose synthase 1
- UniProt
- Q9ZUY6
- Ligands
- NAD, UGA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · resolution 3.47 · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UDP-D-apiose/UDP-D-xylose synthase 1 | protein | 375 | 43% helix, 16% strand | Q9ZUY6 |
| B | UDP-D-apiose/UDP-D-xylose synthase 1 | protein | 367 | 43% helix, 17% strand | Q9ZUY6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- UGA · Uridine-5'-diphosphate-glucuronic acid · ligand · 2 copies · chains A, B
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 | 917 | 0.82 | 0.83 | 91 | NAD, UGA |
| 2 | 859 | 0.81 | 0.83 | 84 | NAD, UGA |
| 3 | 87 | 0.42 | 0.78 | 24 | empty |
| 4 | 82 | 0.41 | 0.78 | 23 | empty |
| 5 | 57 | 0.27 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1950 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6H0P · The structure of C100A mutant of arabidopsis thaliana udp-APIOSE/UDP- xylose synthase in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZUY6 · AlphaFold monomer V2.0 prediction for udp-D-APIOSE/UDP-D-xylose synthase 1 (Q9ZUY6) · 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 Q9ZUY6
- Elsewhere: RCSB PDB 6H0P · PDBe 6H0P · UniProt Q9ZUY6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.