Research workbench
Crystal structure of the tandem DUF26 ectodomain from the Arabidopsis thaliana cysteine-rich receptor-like protein PDLP5.
Analyse Crystal structure of the tandem DUF26 ectodomain from the Arabidopsis thaliana… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GRE
- Type
- protein
- Length
- 412 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.29
- Source
- Arabidopsis thaliana
- Molecule
- Cysteine-rich repeat secretory protein 2
- UniProt
- Q8GUJ2
- Ligands
- AE3, NAG, NA, SO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · resolution 1.29 · 2 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine-rich repeat secretory protein 2 | protein | 205 | 34% helix, 30% strand | Q8GUJ2 |
| B | Cysteine-rich repeat secretory protein 2 | protein | 207 | 32% helix, 30% strand | Q8GUJ2 |
Ligands and binding sites
- AE3 · 2-(2-ethoxyethoxy)ethanol · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.63 | 0.77 | 56 | AE3 |
| 2 | 348 | 0.61 | 0.78 | 47 | EDO, GOL |
| 3 | 56 | 0.27 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 704 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6GRE · Crystal structure of the tandem DUF26 ectodomain from the arabidopsis thaliana… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8GUJ2 · AlphaFold monomer V2.0 prediction for plasmodesmata-located protein 5 (Q8GUJ2) · 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 Q8GUJ2
- Elsewhere: RCSB PDB 6GRE · PDBe 6GRE · UniProt Q8GUJ2
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