SMTL ID : 6bx7.1

Crystal Structure of Human Protocadherin-1 EC1-4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 7 residues within 4Å: Chain A: E.156, A.157, R.186, W.187, S.189, Y.190, D.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.191 Salt bridges: A:E.156, A:E.156 EPE.13: 7 residues within 4Å: Chain B: E.156, A.157, R.186, W.187, S.189, Y.190, D.191 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.191 Salt bridges: B:E.156, B:E.156

22 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: E.10, E.11, D.60, E.62, D.107 Ligands: CA.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.10, A:D.60, A:E.62, A:D.107 CA.3: 9 residues within 4Å: Chain A: E.10, R.61, E.62, D.104, I.105, D.107, N.108, D.140 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.10, A:E.62, A:D.104, A:I.105, A:D.140 CA.4: 6 residues within 4Å: Chain A: N.106, N.108, D.138, D.140, N.144, D.198 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.108, A:D.138, A:D.140, A:N.144, A:D.198 CA.5: 4 residues within 4Å: Chain A: E.123, D.183, E.185, D.219 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.123, A:E.185, A:D.219, H2O.1, H2O.1 CA.6: 6 residues within 4Å: Chain A: E.123, E.185, D.216, T.217, D.219, D.252 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.123, A:E.185, A:E.185, A:D.216, A:D.252 CA.7: 6 residues within 4Å: Chain A: N.218, N.220, D.250, D.252, N.256, D.305 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.220, A:D.250, A:D.252, A:N.256, A:D.305 CA.8: 5 residues within 4Å: Chain A: E.235, D.290, E.292, D.326, N.327 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.235, A:D.290, A:E.292, A:D.326, H2O.1 CA.9: 6 residues within 4Å: Chain A: E.235, E.292, D.323, M.324, D.326, D.367 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.235, A:E.292, A:D.323, A:M.324, A:D.367 CA.10: 6 residues within 4Å: Chain A: N.325, N.327, D.365, D.367, N.371, D.424 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.327, A:D.365, A:D.367, A:N.371, A:D.424 CA.11: 5 residues within 4Å: Chain A: E.350, D.409, Y.410, D.442, V.443 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.350, A:E.350, A:D.409, A:D.442 CA.12: 2 residues within 4Å: Chain A: D.188, S.189 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.188 CA.14: 6 residues within 4Å: Chain B: E.10, E.11, D.60, E.62, D.107 Ligands: CA.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.10, B:D.60, B:E.62, B:D.107 CA.15: 9 residues within 4Å: Chain B: E.10, R.61, E.62, D.104, I.105, D.107, N.108, D.140 Ligands: CA.14 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.10, B:E.62, B:D.104, B:I.105, B:D.140 CA.16: 6 residues within 4Å: Chain B: N.106, N.108, D.138, D.140, N.144, D.198 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.108, B:D.138, B:D.140, B:N.144, B:D.198 CA.17: 4 residues within 4Å: Chain B: E.123, D.183, E.185, D.219 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.123, B:E.185, B:D.219, H2O.1, H2O.2 CA.18: 6 residues within 4Å: Chain B: E.123, E.185, D.216, T.217, D.219, D.252 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.123, B:E.185, B:E.185, B:D.216, B:D.252 CA.19: 6 residues within 4Å: Chain B: N.218, N.220, D.250, D.252, N.256, D.305 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.220, B:D.250, B:D.252, B:N.256, B:D.305 CA.20: 5 residues within 4Å: Chain B: E.235, D.290, E.292, D.326, N.327 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.235, B:D.290, B:E.292, B:D.326, H2O.2 CA.21: 6 residues within 4Å: Chain B: E.235, E.292, D.323, M.324, D.326, D.367 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.235, B:E.292, B:D.323, B:M.324, B:D.367 CA.22: 6 residues within 4Å: Chain B: N.325, N.327, D.365, D.367, N.371, D.424 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.327, B:D.365, B:D.367, B:N.371, B:D.424 CA.23: 5 residues within 4Å: Chain B: E.350, D.409, Y.410, D.442, V.443 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.350, B:E.350, B:D.409, B:D.442 CA.24: 2 residues within 4Å: Chain B: D.188, S.189 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.188

Links

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Citation

Modak, D. et al., Identification of an adhesive interface for the non-clustered delta 1 protocadherin-1 involved in respiratory diseases. Commun Biol (2019)

Release Date

2018-12-19

Peptides

Protocadherin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protocadherin-1