SMTL ID : 6i6h.1

Crystal structure of the KDEL receptor in the peptide bound state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ALA- GLU- LYS- ASP- GLU- LEU: AEKDEL peptide(Non-covalent)

ALA-GLU-LYS-ASP-GLU-LEU.1: 16 residues within 4Å: Chain A: R.5, D.9, R.47, Y.48, S.54, I.56, N.60, M.63, K.64, E.117, W.120, R.159, Y.162, N.165, W.166, R.169 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:I.56, A:K.64 Hydrogen bonds: A:R.5, A:Y.48, A:S.54, A:N.60, A:E.117, A:Y.162, A:N.165 Water bridges: A:R.47, A:D.50, A:D.50, A:S.54, A:K.64, A:K.64, A:E.117, A:Y.158, A:R.159, A:R.159 Salt bridges: A:R.5, A:R.5, A:R.47, A:R.159, A:R.169, A:R.169

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

OLC.2: 7 residues within 4Å: Chain A: L.10, L.13, A.14, I.17, L.21, K.25 Ligands: OLC.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.10, A:L.10, A:L.13, A:I.17, A:L.21 OLC.3: 11 residues within 4Å: Chain A: T.7, F.153, L.157, A.160, L.161, V.164, F.195, V.199 Ligands: OLC.4, OLC.6, OLC.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.7, A:F.153, A:F.153, A:L.157, A:A.160, A:L.161, A:F.195, A:F.195, A:V.199 OLC.4: 11 residues within 4Å: Chain A: T.7, S.11, A.14, I.18, I.147, F.153, F.154, L.157, Y.198 Ligands: OLC.2, OLC.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.7, A:A.14, A:I.18, A:I.147, A:F.154, A:F.154, A:L.157 Hydrogen bonds: A:H.150, A:Y.198, A:Y.198 OLC.5: 3 residues within 4Å: Chain A: M.1, L.6 Ligands: OLC.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.1, A:L.6 OLC.6: 5 residues within 4Å: Chain A: F.195, Y.196, V.199, T.200 Ligands: OLC.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.195, A:V.199, A:T.200 OLC.7: 5 residues within 4Å: Chain A: L.6, I.56, S.57, Y.59 Ligands: OLC.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.6, A:I.56, A:Y.59, A:Y.59, A:Y.59 OLC.8: 13 residues within 4Å: Chain A: F.97, V.109, N.110, H.111, Y.125, S.128, V.129, L.178, I.179, V.182 Ligands: OLC.9, OLC.10, OLC.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.109, A:Y.125, A:V.129, A:V.182 Hydrogen bonds: A:H.111 OLC.9: 3 residues within 4Å: Ligands: OLC.8, OLC.10, OLC.11 No protein-ligand interaction detected (PLIP) OLC.10: 7 residues within 4Å: Chain A: L.105, L.108, V.109, N.110, F.113 Ligands: OLC.8, OLC.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.105 Hydrogen bonds: A:L.108, A:N.110 Water bridges: A:N.110, A:H.111 OLC.11: 8 residues within 4Å: Chain A: V.129, L.132, L.135, F.136, S.139, L.190 Ligands: OLC.8, OLC.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.132, A:L.135, A:F.136, A:L.190 OLC.12: 9 residues within 4Å: Chain A: L.163, W.166, I.167, Y.170, F.176, V.181, V.189, C.192 Ligands: OLC.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.167, A:Y.170, A:Y.170, A:Y.170, A:F.176, A:F.176, A:F.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brauer, P. et al., Structural basis for pH-dependent retrieval of ER proteins from the Golgi by the KDEL receptor. Science (2019)

Release Date

2019-02-27

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