SMTL ID : 5wiv.1

Structure of the sodium-bound human D4 Dopamine receptor in complex with Nemonapride

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

1 x AQD: Nemonapride(Non-covalent)

AQD.1: 21 residues within 4Å: Chain A: V.91, L.94, F.95, L.115, M.116, D.119, V.120, C.123, T.124, C.189, L.191, V.197, S.200, S.201, S.204, W.362, F.365, F.366, H.369, T.389, Y.393 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.91, A:F.95, A:L.115, A:V.120, A:L.191, A:F.365, A:F.365, A:T.389 Hydrogen bonds: A:D.119, A:D.119, A:S.200, A:Y.393 Water bridges: A:L.191 Salt bridges: A:D.119 Halogen bonds: A:V.197

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: Y.147, G.152, S.153, R.155, Q.156 Ligands: PO4.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.147, A:S.153, A:Q.156 Water bridges: A:R.154 Salt bridges: A:R.155 PO4.3: 1 residues within 4Å: Chain A: R.345 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.345 Salt bridges: A:R.345 PO4.4: 2 residues within 4Å: Chain A: L.89, P.93 No protein-ligand interaction detected (PLIP) PO4.5: 5 residues within 4Å: Chain A: P.72, R.137, A.140, R.155 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.155, A:Q.156 Salt bridges: A:R.137 PO4.6: 3 residues within 4Å: Chain A: A.251, D.252, Q.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.252, A:Q.319, A:Q.319 Water bridges: A:D.252

8 x OLA: OLEIC ACID(Non-covalent)

OLA.7: 11 residues within 4Å: Chain A: V.63, Q.70, T.71, S.75, V.78, S.79, A.82, L.86, L.157, W.164 Ligands: PEG.22 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.78, A:A.82, A:L.86, A:L.157, A:W.164 Hydrogen bonds: A:T.71 Water bridges: A:S.75 OLA.8: 11 residues within 4Å: Chain A: Q.37, A.40, G.44, L.47, L.48, A.51, E.99, S.386, W.390, V.394 Ligands: PEG.23 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.51, A:W.390, A:W.390, A:W.390, A:V.394 Hydrogen bonds: A:S.386, A:S.386 OLA.9: 6 residues within 4Å: Chain A: F.128, A.169, V.170, Y.199, C.203, P.208 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.128, A:F.128, A:A.169, A:V.170, A:P.208 OLA.10: 10 residues within 4Å: Chain A: G.55, L.58, V.59, S.62, P.400, T.404, F.410, R.411, V.413, F.414 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.58, A:L.58, A:V.59, A:P.400, A:T.404, A:F.410, A:V.413, A:F.414, A:F.414, A:F.414 Salt bridges: A:R.411 OLA.11: 10 residues within 4Å: Chain A: L.213, Y.216, W.217, F.220, R.345, P.352, V.355, G.356, L.360 Ligands: OLA.13 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.213, A:Y.216, A:F.220, A:F.220, A:V.355, A:L.360 Salt bridges: A:R.345 OLA.12: 4 residues within 4Å: Chain A: F.138, A.142, V.143, L.215 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.138, A:V.143, A:L.215 OLA.13: 7 residues within 4Å: Chain A: P.352, V.353, G.356, A.357, L.360, F.406 Ligands: OLA.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.353, A:A.357, A:L.360, A:F.406 OLA.14: 5 residues within 4Å: Chain A: F.206, V.367, I.370, T.371, L.374 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.367, A:I.370, A:L.374

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.15: 3 residues within 4Å: Chain A: V.367, V.368, L.384 No protein-ligand interaction detected (PLIP) PEG.16: 2 residues within 4Å: Chain A: V.202, I.370 No protein-ligand interaction detected (PLIP) PEG.17: 6 residues within 4Å: Chain A: A.117, M.118, M.121, A.168, A.172, L.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.168 PEG.18: 2 residues within 4Å: Chain A: L.42, P.93 No protein-ligand interaction detected (PLIP) PEG.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.20: 3 residues within 4Å: Chain A: S.108, L.111 Ligands: PEG.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.108 PEG.21: 2 residues within 4Å: Chain A: S.108 Ligands: PEG.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.108 PEG.22: 2 residues within 4Å: Chain A: W.164 Ligands: OLA.7 No protein-ligand interaction detected (PLIP) PEG.23: 2 residues within 4Å: Chain A: A.387 Ligands: OLA.8 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.24: 3 residues within 4Å: Chain A: D.84, S.126, S.396 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.126, A:S.396 Water bridges: A:S.396

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Science (2017)

Release Date

2017-10-18

Peptides

D(4) dopamine receptor, soluble cytochrome b562 chimera: 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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D(4) dopamine receptor, soluble cytochrome b562 chimera

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