MolNFT v1 · #184670 · protein
Crystal structure of the kdel receptor bound to hdel peptide at pH 7.0
7OYE · Er lumen protein-retaining receptor 2: “Crystal structure of the kdel receptor bound to hdel peptide at pH 7.0”. X-ray diffraction, 1 ligand (CO2), 1 pocket (best druggability 0.32). MolNFT v1 #184670 on GenesisL1: 3D structure…
- PDB
- 7OYE
- Type
- protein
- Length
- 215 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Er lumen protein-retaining receptor 2; Thr-ala-glu-his-asp-glu-leu
- UniProt
- Q5ZKX9
- Ligands
- CO2
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Er lumen protein-retaining receptor 2 | protein | 209 | 77% helix, 0% strand | Q5ZKX9 |
| B | Thr-ala-glu-his-asp-glu-leu | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- CO2 · Carbon dioxide · ion · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 555 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7OYE · Crystal structure of the KDEL receptor bound to HDEL peptide at pH 7.0 · 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 7OYE · PDBe 7OYE · UniProt Q5ZKX9
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