SMTL ID : 5k5s.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.1: 12 residues within 4Å: Chain A: R.66, W.70, T.145, G.146, S.147, A.168, S.169, S.170, Y.218, E.297, A.298, I.416 11 PLIP interactions: 9 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:W.70, A:T.145, A:A.298 Hydrogen bonds: A:S.147, A:A.168, A:S.170, A:S.170, A:E.297, W.1, W.1 Water bridges: A:S.170 TRP.13: 12 residues within 4Å: Chain B: R.66, W.70, T.145, G.146, S.147, A.168, S.169, S.170, Y.218, E.297, A.298, I.416 12 PLIP interactions: 10 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:W.70, B:T.145, B:A.298 Hydrogen bonds: B:S.147, B:S.170, B:S.170, B:S.170, B:S.171, B:E.297, W.13, W.13 Water bridges: B:S.170

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

PO4.2: 8 residues within 4Å: Chain A: R.66, R.69, W.70, H.413, L.414, R.415, I.416, S.417 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.413, A:R.415, A:I.416, A:S.417, A:S.417 Salt bridges: A:R.66, A:R.69 PO4.3: 7 residues within 4Å: Chain A: E.191, H.192, T.195, K.225, E.229, K.517, R.520 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.195, A:T.195 Water bridges: A:K.225, A:K.225, A:K.517, A:R.520 Salt bridges: A:H.192, A:K.225, A:K.517, A:R.520 PO4.14: 8 residues within 4Å: Chain B: R.66, R.69, W.70, H.413, L.414, R.415, I.416, S.417 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.415, B:I.416, B:S.417 Salt bridges: B:R.66, B:R.69 PO4.15: 6 residues within 4Å: Chain B: H.192, T.195, K.225, E.229, K.517, R.520 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.195 Water bridges: B:K.225, B:K.517 Salt bridges: B:H.192, B:K.225, B:K.517, B:R.520

8 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: I.81, N.82, S.84, L.87, L.88 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.81, A:S.84, A:L.87, H2O.2 CA.5: 5 residues within 4Å: Chain A: F.38, P.39, T.100, A.144, T.145 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.100, H2O.3 CA.6: 3 residues within 4Å: Chain A: R.66, S.302, S.303 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain A: E.231, D.234 Chain B: G.557 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.231, A:D.234, B:G.557, H2O.12 CA.12: 3 residues within 4Å: Chain A: G.557 Chain B: E.231, D.234 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:G.557, B:E.231, B:D.234 CA.16: 6 residues within 4Å: Chain B: I.81, N.82, S.84, L.87, L.88, P.89 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:I.81, B:S.84, B:L.87, B:L.88, H2O.8 CA.17: 4 residues within 4Å: Chain B: P.39, T.100, A.144, T.145 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.100, H2O.8 CA.18: 3 residues within 4Å: Chain B: F.42, S.302, L.304 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.302, H2O.9, H2O.11

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

NAG.8: 2 residues within 4Å: Chain A: N.90, K.453 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.90, A:K.453 NAG.9: 2 residues within 4Å: Chain A: N.287, T.289 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.287 NAG.10: 4 residues within 4Å: Chain A: K.323, N.488, N.512, Y.514 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.514 Hydrogen bonds: A:N.488 Water bridges: A:N.488 NAG.11: 6 residues within 4Å: Chain A: R.205, N.207, F.539, N.541, R.544, D.545 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.539 Hydrogen bonds: A:N.207, A:N.541 NAG.19: 5 residues within 4Å: Chain B: R.205, N.207, F.539, N.541, D.545 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.539 Hydrogen bonds: B:N.207, B:D.545

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
B

Extracellular calcium-sensing receptor