SMTL ID : 7m3f.1

Asymmetric Activation of the Calcium Sensing Receptor Homodimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.80 Å

Oligo State

homo-dimer

Ligands

3 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: 6 residues within 4Å: Chain A: K.331, E.483, N.496, Y.518, N.520, Y.522 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.518 NAG-NAG.2: 5 residues within 4Å: Chain A: R.213, N.215, F.547, N.549, D.553 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.213 NAG-NAG.3: 5 residues within 4Å: Chain B: R.213, N.215, F.547, N.549, D.553 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.213

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

NAG.4: 2 residues within 4Å: Chain A: V.266, N.269 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.266 Hydrogen bonds: A:N.269 NAG.5: 2 residues within 4Å: Chain A: N.295, H.320 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain A: N.476, Q.484, T.486 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.486 NAG.7: 1 residues within 4Å: Chain A: N.602 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain B: E.265, V.266, N.269 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.266 Hydrogen bonds: B:E.265 NAG.15: 1 residues within 4Å: Chain B: N.295 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.295 NAG.16: 5 residues within 4Å: Chain B: K.331, N.496, Y.518, N.520, Y.522 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.522 Hydrogen bonds: B:N.496 NAG.17: 3 residues within 4Å: Chain B: N.476, Q.484, T.486 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.486 NAG.18: 1 residues within 4Å: Chain B: N.602 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.602

2 x YP4: N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]propan-1-amine(Non-covalent)

YP4.8: 8 residues within 4Å: Chain A: Q.689, F.692, I.785, T.788, W.826, I.830, Y.833, E.845 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.692, A:F.692, A:I.785, A:T.788, A:W.826, A:W.826, A:W.826, A:W.826, A:I.830 Hydrogen bonds: A:Q.689, A:E.845 pi-Stacking: A:F.692, A:Y.833 YP4.19: 8 residues within 4Å: Chain B: Q.689, F.692, L.778, L.781, L.784, I.785, T.788, W.826 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.692, B:F.692, B:L.781, B:L.784, B:I.785, B:T.788, B:W.826, B:W.826 pi-Stacking: B:F.692

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.9: 10 residues within 4Å: Chain A: R.74, T.153, G.154, S.155, A.176, S.177, S.178, Y.226, E.305, A.306 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.153, A:A.176 Hydrogen bonds: A:S.155, A:S.178, A:S.178, A:S.178, W.9 TRP.20: 10 residues within 4Å: Chain B: R.74, T.153, G.154, S.155, A.176, S.177, S.178, Y.226, E.305, A.306 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:T.153 Hydrogen bonds: B:S.155, B:S.178, B:S.178, B:S.178, W.20

4 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain A: I.89, S.92, L.95, L.96 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.92, A:L.95, A:L.96 CA.11: 1 residues within 4Å: Chain A: G.565 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.565 CA.12: 2 residues within 4Å: Chain A: D.242 Chain B: G.565 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.242, B:G.565 CA.21: 3 residues within 4Å: Chain B: I.89, S.92, L.96 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.92, B:L.96

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

PO4.13: 8 residues within 4Å: Chain A: R.74, R.77, W.78, H.421, L.422, R.423, I.424, S.425 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.423, A:I.424, A:S.425, A:S.425 Salt bridges: A:R.74, A:R.77 PO4.22: 8 residues within 4Å: Chain B: R.74, R.77, W.78, H.421, L.422, R.423, I.424, S.425 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.78, B:R.423, B:I.424, B:S.425 Salt bridges: B:R.74, B:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, Y. et al., Asymmetric activation of the calcium-sensing receptor homodimer. Nature (2021)

Release Date

2021-06-30

Peptides

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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Extracellular calcium-sensing receptor

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