SMTL ID : 7m3g.1

Asymmetric Activation of the Calcium Sensing Receptor Homodimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.50 Å

Oligo State

homo-dimer

Ligands

2 x ACE- DCY- DAL- DAR- DAR- DAR- DAL- DAR- NH2: etelcalcetide(Non-covalent)

ACE-DCY-DAL-DAR-DAR-DAR-DAL-DAR-NH2.1: 19 residues within 4Å: Chain A: R.180, S.183, N.197, E.199, K.233, E.236, D.488, C.490, D.492 Chain B: D.223, S.248, E.249, L.250, I.251, S.252, S.255, D.256, E.259, H.262 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:D.223, B:S.248, B:S.252, B:S.255, B:S.255, A:R.180, A:E.199, A:K.233, A:E.236 Salt bridges: B:E.249, B:E.259, A:E.236, A:D.488, A:D.492 ACE-DCY-DAL-DAR-DAR-DAR-DAL-DAR-NH2.2: 20 residues within 4Å: Chain A: D.223, E.249, L.250, I.251, S.252, S.255, D.256, E.258, E.259, H.262 Chain B: R.180, S.183, N.197, E.199, K.233, E.236, D.488, E.489, C.490, D.492 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:R.180, B:K.233, B:E.236, A:S.255, A:S.255, A:E.258, A:E.259, A:H.262 Salt bridges: B:E.236, B:D.488, B:D.492, A:E.249, A:E.259

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

NAG-NAG.3: 2 residues within 4Å: Chain A: V.266, N.269 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 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 NAG-NAG.5: 4 residues within 4Å: Chain B: H.262, E.265, V.266, N.269 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: K.331, N.496, Y.518, N.520, Y.522 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 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

2 x H43: 2-[4-[(3S)-3-[[(1R)-1-naphthalen-1-ylethyl]amino]pyrrolidin-1-yl]phenyl]ethanoic acid(Non-covalent)

H43.8: 12 residues within 4Å: Chain A: Q.689, F.692, G.693, L.781, I.785, T.788, C.789, W.826, I.830, Y.833, E.845, I.849 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.692, A:L.781, A:I.785, A:I.785, A:T.788, A:W.826, A:W.826, A:W.826, A:W.826, A:I.830, A:I.849 Hydrogen bonds: A:Q.689, A:Q.689 pi-Stacking: A:F.692 H43.17: 6 residues within 4Å: Chain B: Q.689, F.692, T.788, W.826, E.845, I.849 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.692, B:T.788, B:W.826, B:W.826, B:I.849 Hydrogen bonds: B:Q.689, B:Q.689 pi-Stacking: B:F.692

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

NAG.9: 3 residues within 4Å: Chain A: N.476, Q.484, T.486 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.486 Hydrogen bonds: A:N.476, A:Q.484 NAG.10: 5 residues within 4Å: Chain A: K.331, N.496, Y.518, N.520, Y.522 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.522 Hydrogen bonds: A:N.496 NAG.11: 2 residues within 4Å: Chain A: E.601, N.602 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain B: N.476, Q.484, T.486 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.486 Hydrogen bonds: B:N.476 NAG.19: 2 residues within 4Å: Chain B: E.601, N.602 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.601, B:E.601, B:N.602

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.12: 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 Hydrogen bonds: A:S.155, A:S.178, A:S.178, A:S.178, A:E.305, W.12 TRP.20: 11 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, I.424 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.153, B:A.306 Hydrogen bonds: B:S.155, B:S.178, B:S.178, B:E.305

4 x CA: CALCIUM ION(Non-covalent)

CA.13: 5 residues within 4Å: Chain A: I.89, N.90, S.92, L.95, L.96 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:I.89, A:S.92, A:L.95 CA.14: 2 residues within 4Å: Chain A: G.565 Chain B: D.242 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:G.565, B:D.242 CA.16: 2 residues within 4Å: Chain A: D.242 Chain B: G.565 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.565 CA.21: 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)

PO4.15: 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:H.421, A:R.423, A:I.424, 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 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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