Research workbench
Crystal structure of the kdel receptor in the peptide bound state
Analyse Crystal structure of the kdel receptor in the peptide bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I6H
- Type
- protein
- Length
- 213 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Er lumen protein-retaining receptor 2; Aekdel peptide
- UniProt
- Q5ZKX9
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Er lumen protein-retaining receptor 2 | protein | 207 | 77% helix, 0% strand | Q5ZKX9 |
| B | Aekdel peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.51 | 0.86 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 584 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6I6H · Crystal structure of the KDEL receptor in the peptide bound state · the same entry in another collection · chain A against A, TM-score 1.00
- Q5ZKX9 · AlphaFold monomer V2.0 prediction for er lumen protein-retaining receptor 2 (Q5ZKX9) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q5ZKX9
- Elsewhere: RCSB PDB 6I6H · PDBe 6I6H · UniProt Q5ZKX9
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