SMTL ID : 6y7v.1

Crystal structure of the KDEL receptor bound to HDEL peptide at pH 6.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

monomer

Ligands

1 x GLU- HIS- ASP- GLU- LEU: GLU-HIS-ASP-GLU-LEU(Non-covalent)

GLU-HIS-ASP-GLU-LEU.1: 19 residues within 4Å: Chain A: R.5, D.9, R.47, Y.48, D.50, S.54, I.56, N.60, M.63, K.64, Y.67, E.117, W.120, R.159, Y.162, N.165, W.166, R.169 Ligands: CO2.8 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.56, A:M.63, A:K.64, A:Y.67 Hydrogen bonds: A:Y.48, A:Y.48, A:S.54, A:N.60, A:Y.162, A:N.165 Water bridges: A:R.47, A:D.50, A:S.54, A:K.64, A:Y.158, A:R.159 Salt bridges: A:R.5, A:R.47, A:R.159, A:R.169, A:R.169 pi-Stacking: A:W.120, A:W.120

6 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.2: 7 residues within 4Å: Chain A: V.109, N.110, H.111, Y.125, I.179, V.182, V.186 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.109, A:I.179, A:V.186, A:V.186 Water bridges: A:N.110, A:N.110 OLC.3: 1 residues within 4Å: Chain A: F.97 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.97, A:F.97 OLC.4: 3 residues within 4Å: Chain A: W.168, Y.171, F.172 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.168, A:F.172, A:F.172 OLC.5: 6 residues within 4Å: Chain A: I.3, F.4, T.7, H.150, Y.198, L.203 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.3, A:T.7 Salt bridges: A:H.150 OLC.6: 5 residues within 4Å: Chain A: L.132, V.189, L.190, C.192, D.193 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.189 Hydrogen bonds: A:C.192, A:D.193 Water bridges: A:F.194 OLC.7: 5 residues within 4Å: Chain A: I.167, F.195, Y.196, V.199, T.200 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.167

1 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.8: 3 residues within 4Å: Chain A: E.117 Ligands: GLU-HIS-ASP-GLU-LEU.1, GLU-HIS-ASP-GLU-LEU.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gerondopoulos, A. et al., A signal capture and proofreading mechanism for the KDEL-receptor explains selectivity and dynamic range in ER retrieval. Elife (2021)

Release Date

2021-02-10

Peptides

ER lumen protein-retaining receptor 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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ER lumen protein-retaining receptor 2

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