SMTL ID : 5fbh.1

Crystal structure of the extracellular domain of human calcium sensing receptor with bound Gd3+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x GD3: GADOLINIUM ION(Non-covalent)

GD3.1: 2 residues within 4Å: Chain A: E.256, E.259 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.256, A:E.256, A:E.259 GD3.10: 2 residues within 4Å: Chain B: E.256, E.259 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.256, B:E.256, B:E.259

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: S.267 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.267, A:S.267, H2O.1 MG.3: 6 residues within 4Å: Chain A: I.108, N.109, S.111, L.114, L.115, L.118 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:I.108, A:L.114, A:L.115 MG.11: 5 residues within 4Å: Chain B: I.108, N.109, S.111, L.114, L.115 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:I.108, B:S.111, B:L.114, B:L.115

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

BCT.4: 7 residues within 4Å: Chain A: R.93, R.96, W.97, L.441, R.442, I.443, S.444 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.93, A:R.96, A:S.444 BCT.12: 8 residues within 4Å: Chain B: R.93, R.96, W.97, H.440, L.441, R.442, I.443, S.444 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.96, B:R.442, B:I.443, B:S.444, B:S.444

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

CL.5: 5 residues within 4Å: Chain A: F.65, P.66, T.127, A.171, T.172 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: F.65, P.66, T.127, A.171, T.172 Ligand excluded by PLIP

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

NAG.6: 3 residues within 4Å: Chain A: H.281, E.284, N.288 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.284 Hydrogen bonds: A:E.284, A:E.284, A:E.284, A:N.288 NAG.7: 1 residues within 4Å: Chain A: N.314 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain A: N.495 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.495 NAG.14: 4 residues within 4Å: Chain B: H.281, E.284, V.285, N.288 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.284, B:V.285 Hydrogen bonds: B:E.284, B:N.288 NAG.15: 1 residues within 4Å: Chain B: N.314 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.314 NAG.16: 2 residues within 4Å: Chain B: N.495, T.505 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.505 Hydrogen bonds: B:N.495 NAG.17: 3 residues within 4Å: Chain B: N.515, N.539, Y.541 No protein-ligand interaction detected (PLIP)

2 x TCR: CYCLOMETHYLTRYPTOPHAN(Non-covalent)

TCR.9: 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 6 PLIP interactions: 6 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 TCR.18: 12 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, I.443 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.97, B:T.172, B:A.325, B:I.443 Hydrogen bonds: B:S.174, B:S.197, B:S.197

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
B

B
A

Extracellular calcium-sensing receptor

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