SMTL ID : 7m3e.1

Asymmetric Activation of the Calcium Sensing Receptor Homodimer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

1 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: R.213, N.215, F.547, N.549, D.553 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.213, A:R.213

2 x YP1: 2-chloro-6-[(2R)-2-hydroxy-3-{[2-methyl-1-(naphthalen-2-yl)propan-2-yl]amino}propoxy]benzonitrile(Non-covalent)

YP1.2: 11 residues within 4Å: Chain A: F.676, Q.689, F.692, I.785, F.822, W.826, F.829, I.830, Y.833, E.845, A.848 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.676, A:F.692, A:F.692, A:F.822, A:F.822, A:W.826, A:W.826, A:F.829, A:F.829, A:I.830, A:Y.833, A:A.848 Hydrogen bonds: A:Q.689, A:Q.689, A:E.845, A:E.845 YP1.12: 11 residues within 4Å: Chain B: F.676, Q.689, F.692, I.785, F.822, W.826, F.829, I.830, Y.833, E.845, A.848 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.676, B:F.692, B:F.692, B:F.692, B:F.822, B:F.822, B:W.826, B:W.826, B:F.829, B:F.829, B:I.830, B:Y.833, B:A.848 Hydrogen bonds: B:Q.689, B:Q.689, B:E.845, B:E.845

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

NAG.3: 3 residues within 4Å: Chain A: E.265, V.266, N.269 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.266 Hydrogen bonds: A:E.265, A:N.269 NAG.4: 1 residues within 4Å: Chain A: N.295 No protein-ligand interaction detected (PLIP) NAG.5: 5 residues within 4Å: Chain A: K.331, N.496, Y.518, N.520, Y.522 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.331 NAG.6: 2 residues within 4Å: Chain A: N.476, Q.484 No protein-ligand interaction detected (PLIP) NAG.13: 6 residues within 4Å: Chain B: R.213, N.215, F.547, N.549, D.553, D.586 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.213, B:R.213, B:N.215, B:N.549 NAG.14: 4 residues within 4Å: Chain B: H.262, E.265, V.266, N.269 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.265, B:E.265 NAG.15: 2 residues within 4Å: Chain B: N.295, T.297 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: 2 residues within 4Å: Chain B: N.476, T.486 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.486 Hydrogen bonds: B:N.476

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.7: 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.7 TRP.18: 9 residues within 4Å: Chain B: R.74, W.78, T.153, S.155, A.176, S.178, Y.226, E.305, A.306 7 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain B Hydrogen bonds: W.18, B:S.155, B:S.178, B:S.178, B:S.178 Hydrophobic interactions: B:W.78, B:T.153

4 x CA: CALCIUM ION(Non-covalent)

CA.8: 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.9: 2 residues within 4Å: Chain A: D.242 Chain B: G.565 No protein-ligand interaction detected (PLIP) CA.10: 2 residues within 4Å: Chain A: G.565 Chain B: D.242 No protein-ligand interaction detected (PLIP) CA.19: 5 residues within 4Å: Chain B: I.89, N.90, S.92, L.95, L.96 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:I.89, B:S.92, B:L.95

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

PO4.11: 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 PO4.20: 8 residues within 4Å: Chain B: R.74, R.77, W.78, H.421, L.422, R.423, I.424, S.425 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: 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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