SMTL ID : 7oxe.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

monomer

Ligands

1 x ALA- GLU- HIS- ASP- GLU- PHE: THR-ALA-GLU-HIS-ASP-GLU-PHE(Non-covalent)

ALA-GLU-HIS-ASP-GLU-PHE.1: 18 residues within 4Å: Chain A: R.5, D.9, R.47, Y.48, D.50, S.54, I.56, Y.59, N.60, M.63, Y.67, E.117, W.120, R.159, Y.162, N.165, W.166, R.169 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.59, A:M.63, A:Y.67, A:Y.162 Hydrogen bonds: A:R.5, A:R.5, A:Y.48, A:S.54, A:Y.162, A:N.165 Water bridges: A:R.47, A:N.60, A:N.60, A:K.64, A:Y.158, A:R.159 Salt bridges: A:R.47, A:R.159, A:R.169, A:R.169 pi-Stacking: A:W.120, A:W.120 pi-Cation interactions: A:R.5

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

OLC.2: 11 residues within 4Å: Chain A: F.93, V.129, L.132, V.181, V.182, V.185, V.186, V.189, L.190 Ligands: OLC.3, OLC.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.182, A:V.185, A:L.190 OLC.3: 18 residues within 4Å: Chain A: F.97, L.98, P.101, V.102, L.105, V.109, N.110, H.111, Y.125, S.128, V.129, L.178, I.179, V.182, A.183, V.186 Ligands: OLC.2, OLC.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.109, A:Y.125, A:Y.125, A:V.129, A:V.182, A:A.183 Hydrogen bonds: A:H.111 OLC.4: 5 residues within 4Å: Chain A: L.178, V.182, V.186 Ligands: OLC.2, OLC.3 No protein-ligand interaction detected (PLIP) OLC.5: 12 residues within 4Å: Chain A: I.3, F.4, T.7, L.10, S.11, A.14, I.18, I.147, H.150, F.154, L.157, L.161 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.10, A:A.14, A:I.147, A:F.154, A:L.157 Hydrogen bonds: A:T.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newstead, S. et al., Crystal structure of the KDEL receptor bound to HDEF peptide at pH 6.0. To Be Published

Release Date

2022-07-13

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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