SMTL ID : 6cv7.1

Mouse Protocadherin-15 Extracellular Cadherin Domains 1 through 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.27, E.28, D.83, D.85, D.121 Ligands: CA.2 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.27, A:E.28, A:D.83, A:D.85, A:D.121, H2O.14 CA.2: 7 residues within 4Å: Chain A: E.27, D.85, D.118, R.119, D.121, D.159 Ligands: CA.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.27, A:D.85, A:D.85, A:D.118, A:D.159 CA.3: 6 residues within 4Å: Chain A: N.120, N.122, D.157, D.159, N.163, D.215 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.122, A:D.157, A:D.159, A:N.163, A:D.215 CA.4: 5 residues within 4Å: Chain A: E.137, D.236, G.237, D.239, D.289 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.137, A:D.236, A:G.237, A:D.239, A:D.289, H2O.15 CA.5: 5 residues within 4Å: Chain A: D.238, L.240, D.287, D.289, Q.348 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.238, A:L.240, A:D.287, A:D.289, H2O.1 CA.19: 6 residues within 4Å: Chain B: E.27, E.28, D.83, D.85, D.121 Ligands: CA.20 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.27, B:E.28, B:D.83, B:D.85, B:D.121, H2O.33 CA.20: 7 residues within 4Å: Chain B: E.27, D.85, D.118, R.119, D.121, D.159 Ligands: CA.19 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.27, B:D.85, B:D.85, B:D.118, B:D.159 CA.21: 6 residues within 4Å: Chain B: N.120, N.122, D.157, D.159, N.163, D.215 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.122, B:D.157, B:D.159, B:N.163, B:D.215 CA.22: 5 residues within 4Å: Chain B: E.137, D.236, G.237, D.239, D.289 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.137, B:D.236, B:G.237, B:D.239, B:D.289, H2O.34 CA.23: 5 residues within 4Å: Chain B: D.238, L.240, D.287, D.289, Q.348 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.238, B:L.240, B:D.287, B:D.289, H2O.20

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 3 residues within 4Å: Chain A: I.170, N.180 Ligands: NAG.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.180, A:N.180 EDO.7: 4 residues within 4Å: Chain A: V.60, W.63, I.90, S.92 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.60, A:V.94, A:V.94 EDO.8: 4 residues within 4Å: Chain A: F.126, K.127, H.128, E.129 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.126 EDO.9: 4 residues within 4Å: Chain A: N.38, V.69, K.70, Q.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.38, A:Q.71 Water bridges: A:Q.71 EDO.10: 5 residues within 4Å: Chain A: L.65, L.66, D.67, F.74 Ligands: NAG.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.66 EDO.24: 3 residues within 4Å: Chain B: I.170, N.180 Ligands: NAG.36 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.180, B:N.180 EDO.25: 4 residues within 4Å: Chain B: V.60, W.63, I.90, S.92 3 PLIP interactions: 3 interactions with chain B Water bridges: B:V.60, B:V.94, B:V.94 EDO.26: 4 residues within 4Å: Chain B: F.126, K.127, H.128, E.129 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.126 EDO.27: 4 residues within 4Å: Chain B: N.38, V.69, K.70, Q.71 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.38, B:Q.71 Water bridges: B:Q.71 EDO.28: 5 residues within 4Å: Chain B: L.65, L.66, D.67, F.74 Ligands: NAG.34 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.66

10 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.11: 4 residues within 4Å: Chain A: G.142, T.144, N.192, V.194 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.192 Water bridges: A:G.142, A:G.142, A:T.144, A:T.144 MAN.12: 5 residues within 4Å: Chain A: Q.171, Q.212, N.214, R.223, T.225 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.171, A:Q.212, A:R.223 Water bridges: A:N.214, A:R.223 MAN.13: 3 residues within 4Å: Chain A: I.210, T.227 Ligands: MAN.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.227 MAN.14: 5 residues within 4Å: Chain A: E.175, I.210, T.229 Ligands: MAN.13, MAN.15 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.175, A:E.175, A:E.175 MAN.15: 7 residues within 4Å: Chain A: S.130, Y.131, Y.132, Y.208, T.229, T.231 Ligands: MAN.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.229 Water bridges: A:T.229 MAN.29: 4 residues within 4Å: Chain B: G.142, T.144, N.192, V.194 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.192 Water bridges: B:G.142, B:G.142, B:T.144, B:T.144 MAN.30: 5 residues within 4Å: Chain B: Q.171, Q.212, N.214, R.223, T.225 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.171, B:Q.212, B:R.223 Water bridges: B:N.214, B:R.223 MAN.31: 3 residues within 4Å: Chain B: I.210, T.227 Ligands: MAN.32 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.227 MAN.32: 5 residues within 4Å: Chain B: E.175, I.210, T.229 Ligands: MAN.31, MAN.33 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.175, B:E.175 MAN.33: 7 residues within 4Å: Chain B: S.130, Y.131, Y.132, Y.208, T.229, T.231 Ligands: MAN.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.229 Water bridges: B:T.229

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

NAG.16: 6 residues within 4Å: Chain A: N.31, G.32, L.65, F.74, T.78 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.31, A:T.78 Water bridges: A:G.32, A:T.78 NAG.17: 5 residues within 4Å: Chain A: D.61, Y.62, L.65, N.76, R.80 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.65 Hydrogen bonds: A:N.76 Water bridges: A:R.80 NAG.18: 5 residues within 4Å: Chain A: Y.172, N.180, D.181, R.196 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.180, A:D.181 NAG.34: 6 residues within 4Å: Chain B: N.31, G.32, L.65, F.74, T.78 Ligands: EDO.28 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.31, B:T.78, B:T.78 Water bridges: B:G.32, B:T.78 NAG.35: 5 residues within 4Å: Chain B: D.61, Y.62, L.65, N.76, R.80 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.65 Hydrogen bonds: B:N.76 Water bridges: B:R.80 NAG.36: 5 residues within 4Å: Chain B: Y.172, N.180, D.181, R.196 Ligands: EDO.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.180, B:D.181, B:D.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dionne, G. et al., Mechanotransduction by PCDH15 Relies on a Novel cis-Dimeric Architecture. Neuron (2018)

Release Date

2018-08-01

Peptides

Protocadherin-15: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protocadherin-15