MolNFT v1 · #170447 · protein

Crystal structure of the kdel receptor bound to hdel peptide at pH 6.0

6Y7V · Er lumen protein-retaining receptor 2: “Crystal structure of the kdel receptor bound to hdel peptide at pH 6.0”. X-ray diffraction, 1 ligand (CO2). MolNFT v1 #170447 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Y7V
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; Glu-his-asp-glu-leu
UniProt: Q5ZKX9
Ligands: CO2

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	210	76% helix, 0% strand	Q5ZKX9
B	Glu-his-asp-glu-leu	protein	5	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 · 6 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

1 interface between chains.

A–B · 567 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6Y7V · Crystal structure of the KDEL receptor bound to HDEL peptide at pH 6.0 · 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 6Y7V · PDBe 6Y7V · UniProt Q5ZKX9

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