SMTL ID : 5k5t.2 (2 other biounits)

Crystal structure of the inactive form of human calcium-sensing receptor extracellular domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: P.39, T.100, A.144, T.145 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.100 CA.12: 4 residues within 4Å: Chain B: P.39, T.100, A.144, T.145 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.100

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 9 residues within 4Å: Chain A: R.66, R.69, W.70, H.413, L.414, R.415, I.416, S.417 Ligands: SO4.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.70, A:H.413, A:R.415, A:I.416, A:S.417 Salt bridges: A:R.66, A:R.69 SO4.3: 6 residues within 4Å: Chain A: R.66, D.410, Y.411, T.412, H.413 Ligands: SO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.412, A:T.412, A:T.412, A:H.413 Salt bridges: A:R.66 SO4.4: 3 residues within 4Å: Chain A: I.61, R.62, Y.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.61, A:Y.63 Salt bridges: A:R.62 SO4.13: 9 residues within 4Å: Chain B: R.66, R.69, W.70, H.413, L.414, R.415, I.416, S.417 Ligands: SO4.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.70, B:H.413, B:R.415, B:I.416, B:S.417 Salt bridges: B:R.66, B:R.69 SO4.14: 6 residues within 4Å: Chain B: R.66, D.410, Y.411, T.412, H.413 Ligands: SO4.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.412, B:T.412, B:T.412, B:H.413 Salt bridges: B:R.66 SO4.15: 3 residues within 4Å: Chain B: I.61, R.62, Y.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.61, B:Y.63 Salt bridges: B:R.62

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

NAG.5: 2 residues within 4Å: Chain A: E.257, N.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.257 NAG.6: 2 residues within 4Å: Chain A: N.287, H.312 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain A: N.446 Chain B: K.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.446 NAG.8: 3 residues within 4Å: Chain A: N.468, Q.476, Y.514 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.468, A:Y.514 NAG.9: 6 residues within 4Å: Chain A: K.323, E.475, Q.476, G.487, N.488, N.512 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.323, A:E.475, A:Q.476, A:Q.476, A:N.488, A:N.488 NAG.10: 5 residues within 4Å: Chain A: R.205, N.207, F.539, N.541, D.545 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.539 Hydrogen bonds: A:N.207 NAG.11: 2 residues within 4Å: Chain A: N.594, T.596 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.596 NAG.16: 2 residues within 4Å: Chain B: E.257, N.261 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.257 NAG.17: 2 residues within 4Å: Chain B: N.287, H.312 No protein-ligand interaction detected (PLIP) NAG.18: 2 residues within 4Å: Chain A: K.52 Chain B: N.446 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.446 NAG.19: 3 residues within 4Å: Chain B: N.468, Q.476, Y.514 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.468, B:Y.514 NAG.20: 6 residues within 4Å: Chain B: K.323, E.475, Q.476, G.487, N.488, N.512 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.323, B:E.475, B:Q.476, B:Q.476, B:N.488, B:N.488 NAG.21: 5 residues within 4Å: Chain B: R.205, N.207, F.539, N.541, D.545 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.539 Hydrogen bonds: B:N.207 NAG.22: 2 residues within 4Å: Chain B: N.594, T.596 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.596

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Geng, Y. et al., Structural mechanism of ligand activation in human calcium-sensing receptor. Elife (2016)

Release Date

2016-08-03

Peptides

Extracellular calcium-sensing receptor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Extracellular calcium-sensing receptor

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