SMTL ID : 7sil.1

Structure of positive allosteric modulator-bound active human calcium-sensing receptor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: K.323, N.488, Y.510, N.512, Y.514 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: E.202, R.205, N.207, F.539, N.541, D.545 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: K.323, N.488, Y.510, N.512, Y.514 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.512 NAG-NAG.4: 6 residues within 4Å: Chain B: R.205, N.207, F.539, N.541, D.545, D.578 No protein-ligand interaction detected (PLIP)

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 3 residues within 4Å: Chain A: E.257, V.258, N.261 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.257, A:V.258 Hydrogen bonds: A:N.261 NAG.6: 2 residues within 4Å: Chain A: N.287, T.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.287, A:T.289 NAG.7: 3 residues within 4Å: Chain A: N.468, Q.476, T.478 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.478 NAG.19: 2 residues within 4Å: Chain B: V.258, N.261 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.258 Hydrogen bonds: B:N.261 NAG.20: 2 residues within 4Å: Chain B: N.287, T.289 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.287 NAG.21: 3 residues within 4Å: Chain B: N.468, Q.476, T.478 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.478 Hydrogen bonds: B:N.468

2 x TCR: CYCLOMETHYLTRYPTOPHAN(Non-covalent)

TCR.8: 11 residues within 4Å: Chain A: R.66, W.70, T.145, G.146, S.147, A.168, S.169, S.170, Y.218, E.297, A.298 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.70, A:T.145, A:A.298 Hydrogen bonds: A:S.147, A:A.168, A:S.170, A:E.297 TCR.22: 11 residues within 4Å: Chain B: R.66, W.70, T.145, G.146, S.147, A.168, S.169, S.170, Y.218, E.297, A.298 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.70, B:T.145, B:A.298 Hydrogen bonds: B:S.147, B:A.168, B:S.170, B:E.297

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

PO4.9: 8 residues within 4Å: Chain A: R.66, R.69, W.70, H.413, L.414, R.415, I.416, S.417 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.70, A:H.413, A:H.413, A:R.415, A:I.416, A:S.417 Salt bridges: A:R.66, A:R.69 PO4.23: 8 residues within 4Å: Chain B: R.66, R.69, W.70, H.413, L.414, R.415, I.416, S.417 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:W.70, B:H.413, B:H.413, B:R.415, B:I.416, B:S.417 Salt bridges: B:R.66, B:R.69

8 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain A: I.81, N.82, S.84, L.87, L.88 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:I.81, A:S.84, A:L.87 CA.11: 7 residues within 4Å: Chain A: L.37, F.38, P.39, T.100, A.144, T.145, Y.167 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.100 CA.12: 3 residues within 4Å: Chain A: F.42, G.273, S.302 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.302 CA.13: 2 residues within 4Å: Chain A: G.557 Chain B: D.234 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.557 CA.24: 5 residues within 4Å: Chain B: I.81, N.82, S.84, L.87, L.88 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:I.81, B:S.84, B:L.87 CA.25: 7 residues within 4Å: Chain B: L.37, F.38, P.39, T.100, A.144, T.145, Y.167 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.100 CA.26: 3 residues within 4Å: Chain B: F.42, G.273, S.302 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.302 CA.27: 3 residues within 4Å: Chain B: G.557, E.558, P.559 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.557

2 x 9IG: 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine(Non-covalent)

9IG.14: 10 residues within 4Å: Chain A: F.668, Q.681, F.684, G.685, L.773, L.776, I.777, T.780, W.818, E.837 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.668, A:F.684, A:L.776, A:W.818 Hydrogen bonds: A:Q.681 pi-Stacking: A:F.684 9IG.28: 9 residues within 4Å: Chain B: F.668, Q.681, F.684, L.773, L.776, I.777, T.780, W.818, E.837 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.668, B:F.684, B:L.776, B:I.777, B:I.777, B:W.818 Hydrogen bonds: B:Q.681, B:Q.681 pi-Stacking: B:F.684

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.15: 10 residues within 4Å: Chain A: F.821, F.832, V.836, I.839, A.843 Chain B: I.819, P.823, A.826 Ligands: CLR.17, CLR.31 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.821, A:F.832, A:V.836, A:A.843, B:I.819, B:P.823, B:P.823 CLR.16: 11 residues within 4Å: Chain A: L.812, I.816, S.820 Chain B: F.809, L.812, I.813, I.816, V.817 Ligands: CLR.29, CLR.30, CLR.31 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.809, B:L.812, B:I.813, B:I.813, B:I.816, B:V.817, A:L.812, A:I.816 CLR.17: 9 residues within 4Å: Chain A: F.806, I.813, A.843, F.846, G.847, A.850, C.851 Ligands: CLR.15, CLR.31 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.806, A:I.813, A:F.846, A:A.850 CLR.18: 6 residues within 4Å: Chain A: C.781, A.785, F.788, F.789, F.792, I.819 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.785, A:F.788, A:F.788, A:I.819, A:I.819 CLR.29: 8 residues within 4Å: Chain A: I.819, P.823, A.826 Chain B: F.821, F.832, I.839 Ligands: CLR.16, CLR.30 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.819, A:P.823, A:P.823, B:F.821, B:F.832, B:I.839 CLR.30: 5 residues within 4Å: Chain B: F.806, I.813, A.850 Ligands: CLR.16, CLR.29 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.806, B:I.813, B:I.813, B:A.850 CLR.31: 11 residues within 4Å: Chain A: F.809, L.812, I.813, I.816, V.817 Chain B: L.812, I.816, S.820 Ligands: CLR.15, CLR.16, CLR.17 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.809, A:F.809, A:L.812, A:I.813, A:I.813, A:I.816, A:V.817, B:L.812, B:I.816 CLR.32: 6 residues within 4Å: Chain B: C.781, A.785, F.788, F.789, F.792, I.819 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.785, B:F.788, B:F.788, B:F.789, B:I.819, B:I.819

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., Symmetric activation and modulation of the human calcium-sensing receptor. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2022-01-19

Peptides

Isoform 1 of Extracellular calcium-sensing receptor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Isoform 1 of Extracellular calcium-sensing receptor

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