SMTL ID : 9c2f.1

Structure of Calcium-Sensing Receptor in complex with positive allosteric modulator '54149

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

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 B: R.197, N.199, F.531, N.533, D.537 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: N.482, Q.490 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.482 NAG.9: 6 residues within 4Å: Chain A: K.337, E.489, N.502, Y.524, N.526, Y.528 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.528 Hydrogen bonds: A:K.337, A:N.502, A:Y.524 NAG.10: 5 residues within 4Å: Chain A: R.219, N.221, F.553, N.555, D.559 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.553 Hydrogen bonds: A:R.219, A:N.221, A:N.555 NAG.12: 2 residues within 4Å: Chain B: N.460, Q.468 No protein-ligand interaction detected (PLIP) NAG.13: 6 residues within 4Å: Chain B: K.315, E.467, N.480, Y.502, N.504, Y.506 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.506 Hydrogen bonds: B:N.480

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: I.95, N.96, S.98, L.101, L.102 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:I.95, A:S.98, A:L.101, A:L.102 CA.4: 5 residues within 4Å: Chain A: P.53, T.114, A.158, T.159, G.160 No protein-ligand interaction detected (PLIP) CA.5: 1 residues within 4Å: Chain A: R.80 No protein-ligand interaction detected (PLIP) CA.11: 1 residues within 4Å: Chain B: G.549 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.549 CA.15: 4 residues within 4Å: Chain B: I.73, N.74, S.76, L.80 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.76, B:L.80 CA.16: 2 residues within 4Å: Chain A: G.571 Chain B: D.226 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.226, B:D.226 CA.17: 4 residues within 4Å: Chain B: P.31, T.92, A.136, T.137 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.92 CA.18: 2 residues within 4Å: Chain B: R.58, S.294 No protein-ligand interaction detected (PLIP)

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.6: 10 residues within 4Å: Chain A: R.80, T.159, G.160, S.161, A.182, S.183, S.184, Y.232, E.311, A.312 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:T.159 Hydrogen bonds: A:S.161, A:S.184, A:E.311, A:E.311 TRP.14: 10 residues within 4Å: Chain B: T.137, G.138, S.139, A.160, S.161, S.162, Y.210, E.289, A.290, I.408 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:T.137 Hydrogen bonds: B:S.139, B:S.162, B:E.289, B:E.289

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

PO4.7: 8 residues within 4Å: Chain A: R.80, R.83, W.84, H.427, L.428, R.429, I.430, S.431 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.429, A:I.430, A:S.431 Salt bridges: A:R.80, A:R.83 PO4.19: 8 residues within 4Å: Chain B: R.58, R.61, W.62, H.405, L.406, R.407, I.408, S.409 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.62, B:R.407, B:I.408, B:S.409 Salt bridges: B:R.58, B:R.61

2 x 01: (1R)-1-(2H-1,3-benzodioxol-4-yl)-N-[2-(1,2-benzothiazol-3-yl)ethyl]ethan-1-amine

01.8: 10 residues within 4Å: Chain A: Q.695, F.698, G.699, I.791, T.794, W.832, F.835, Y.839, E.851, I.855 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.698, A:T.794, A:W.832, A:I.855 pi-Stacking: A:F.698, A:F.835, A:Y.839 01.20: 8 residues within 4Å: Chain B: Q.673, F.676, G.677, I.769, T.772, Y.817, E.829, I.833 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.817, B:I.833 Hydrogen bonds: B:Q.673, B:E.829 pi-Stacking: B:F.676

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, F. et al., Large library docking identifies positive allosteric modulators of the calcium-sensing receptor. Science (2024)

Release Date

2024-10-02

Peptides

Extracellular calcium-sensing receptor: A
Extracellular calcium-sensing receptor: B

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

Extracellular calcium-sensing receptor

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