Research workbench
Crystal structure of the tandem DUF26 ectodomain from the Arabidopsis thaliana cysteine-rich receptor-like protein PDLP8.
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
- 6GRF
- Type
- protein
- Length
- 627 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Arabidopsis thaliana
- Molecule
- Cysteine-rich repeat secretory protein 15
- UniProt
- Q6NKQ9
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · resolution 1.95 · 3 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine-rich repeat secretory protein 15 | protein | 210 | 32% helix, 31% strand | Q6NKQ9 |
| B | Cysteine-rich repeat secretory protein 15 | protein | 211 | 32% helix, 31% strand | Q6NKQ9 |
| C | Cysteine-rich repeat secretory protein 15 | protein | 206 | 33% helix, 32% strand | Q6NKQ9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-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
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.45 | 0.74 | 30 | empty |
| 2 | 148 | 0.40 | 0.74 | 21 | empty |
| 3 | 115 | 0.40 | 0.75 | 20 | empty |
| 4 | 144 | 0.39 | 0.73 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 382 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 141 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 17 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6GRF · 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
- Q6NKQ9 · AlphaFold monomer V2.0 prediction for plasmodesmata-located protein 8 (Q6NKQ9) · 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 Q6NKQ9
- Elsewhere: RCSB PDB 6GRF · PDBe 6GRF · UniProt Q6NKQ9
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