SMTL ID : 5fbk.1

Crystal structure of the extracellular domain of human calcium sensing receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x TCR: CYCLOMETHYLTRYPTOPHAN(Non-covalent)

TCR.1: 11 residues within 4Å: Chain A: R.93, W.97, T.172, G.173, S.174, A.195, S.196, S.197, Y.245, E.324, A.325 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.97, A:T.172, A:A.325 Hydrogen bonds: A:S.174, A:A.195, A:S.197, A:S.198, A:E.324 Water bridges: A:G.175 TCR.11: 11 residues within 4Å: Chain B: R.93, W.97, T.172, G.173, S.174, A.195, S.196, S.197, Y.245, E.324, A.325 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.97, B:T.172, B:A.325 Hydrogen bonds: B:S.174, B:A.195, B:S.197, B:S.197, B:S.198, B:E.324 Water bridges: B:G.175

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

NAG.2: 5 residues within 4Å: Chain A: K.350, E.502, N.515, N.539, Y.541 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.350, A:E.502, A:N.515, A:Y.541 NAG.3: 3 residues within 4Å: Chain A: N.495, Q.503, T.505 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.505 Hydrogen bonds: A:N.495, A:Q.503 NAG.4: 1 residues within 4Å: Chain A: N.314 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.314 NAG.5: 4 residues within 4Å: Chain A: H.281, E.284, V.285, N.288 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.284, A:V.285 Hydrogen bonds: A:E.284, A:E.284, A:N.288 NAG.12: 5 residues within 4Å: Chain B: V.513, G.514, N.515, N.539, Y.541 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.513, B:Y.541 Water bridges: B:N.515, B:N.515, B:N.515 NAG.13: 2 residues within 4Å: Chain B: N.495, Q.503 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.495 NAG.14: 1 residues within 4Å: Chain B: N.314 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain B: H.281, E.284, N.288 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.284 Hydrogen bonds: B:E.284, B:E.284, B:N.288

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 7 residues within 4Å: Chain A: L.64, F.65, P.66, T.127, A.171, T.172, Y.194 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: A.181, G.185, F.207, K.208, S.209, F.210 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: P.301, S.329 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain B: F.65, P.66, T.127, A.171, T.172, Y.194 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain B: A.181, G.185, F.207, K.208, S.209, F.210 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: F.69, S.329 Ligand excluded by PLIP

2 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.9: 7 residues within 4Å: Chain A: R.93, R.96, W.97, L.441, R.442, I.443, S.444 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.96, A:R.442, A:S.444, A:S.444 BCT.19: 7 residues within 4Å: Chain B: R.93, R.96, W.97, L.441, R.442, I.443, S.444 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.93, B:R.93, B:R.96, B:R.96, B:S.444

3 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain A: I.108, N.109, S.111, L.114, L.115 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.108, A:S.111, A:L.114, H2O.2 MG.20: 1 residues within 4Å: Chain B: S.267 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.267, B:S.267, H2O.2, H2O.10, H2O.11, H2O.12 MG.21: 5 residues within 4Å: Chain B: I.108, N.109, S.111, L.114, L.115 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:I.108, B:S.111, B:L.114, H2O.9, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, C. et al., Structural basis for regulation of human calcium-sensing receptor by magnesium ions and an unexpected tryptophan derivative co-agonist. Sci Adv (2016)

Release Date

2016-06-22

Peptides

Extracellular calcium-sensing receptor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Extracellular calcium-sensing receptor

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