SMTL ID : 5k8r.1

Structure of human clustered protocadherin gamma B3 EC1-4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

18 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: N.97, N.99, D.129, D.131, N.135, D.186 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.99, A:D.129, A:D.131, A:N.135, A:D.186 CA.2: 6 residues within 4Å: Chain A: E.9, E.10, D.61, E.63, D.98 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.10, A:D.61, A:E.63, A:D.98 CA.3: 8 residues within 4Å: Chain A: E.9, E.63, D.95, I.96, D.98, N.99, D.131 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.63, A:I.96, A:D.98, A:D.131 CA.4: 6 residues within 4Å: Chain A: N.311, N.313, D.343, D.345, N.349, D.396 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.313, A:D.343, A:D.345, A:N.349, A:D.396 CA.5: 8 residues within 4Å: Chain A: E.223, E.280, D.309, E.310, D.312, N.313, D.345 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.223, A:E.280, A:E.280, A:D.309, A:D.345 CA.6: 6 residues within 4Å: Chain A: E.223, D.278, E.280, D.312, N.313 Ligands: CA.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.223, A:D.278, A:E.280, A:D.312, H2O.1 CA.7: 6 residues within 4Å: Chain A: N.206, N.208, D.238, D.240, N.244, D.293 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.208, A:D.238, A:D.240, A:N.244, A:D.293 CA.8: 6 residues within 4Å: Chain A: E.114, D.171, E.173, D.207, N.208 Ligands: CA.9 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.114, A:D.171, A:E.173, A:D.207, H2O.3 CA.9: 8 residues within 4Å: Chain A: E.114, E.173, D.204, A.205, D.207, N.208, D.240 Ligands: CA.8 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.173, A:D.204, A:A.205, A:D.207, A:D.240 CA.15: 6 residues within 4Å: Chain B: N.97, N.99, D.129, D.131, N.135, D.186 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.99, B:D.129, B:D.131, B:N.135, B:D.186 CA.16: 6 residues within 4Å: Chain B: E.9, E.10, D.61, E.63, D.98 Ligands: CA.17 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.10, B:D.61, B:E.63, B:D.98 CA.17: 8 residues within 4Å: Chain B: E.9, E.63, D.95, I.96, D.98, N.99, D.131 Ligands: CA.16 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.63, B:I.96, B:D.98, B:D.131 CA.18: 6 residues within 4Å: Chain B: N.311, N.313, D.343, D.345, N.349, D.396 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.313, B:D.343, B:D.345, B:N.349, B:D.396 CA.19: 8 residues within 4Å: Chain B: E.223, E.280, D.309, E.310, D.312, N.313, D.345 Ligands: CA.20 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.223, B:E.280, B:E.280, B:D.309, B:D.345 CA.20: 6 residues within 4Å: Chain B: E.223, D.278, E.280, D.312, N.313 Ligands: CA.19 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.223, B:D.278, B:E.280, B:D.312, H2O.5 CA.21: 6 residues within 4Å: Chain B: N.206, N.208, D.238, D.240, N.244, D.293 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.208, B:D.238, B:D.240, B:N.244, B:D.293 CA.22: 6 residues within 4Å: Chain B: E.114, D.171, E.173, D.207, N.208 Ligands: CA.23 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.114, B:D.171, B:E.173, B:D.207, H2O.8 CA.23: 8 residues within 4Å: Chain B: E.114, E.173, D.204, A.205, D.207, N.208, D.240 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.173, B:D.204, B:A.205, B:D.207, B:D.240

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

CL.10: 2 residues within 4Å: Chain A: R.34, N.85 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: V.258, R.282 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain B: R.34, N.85 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: V.258, R.282 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.12: 3 residues within 4Å: Chain A: E.328, D.329, L.380 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.380 NA.26: 3 residues within 4Å: Chain B: E.328, D.329, L.380 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.380

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

EPE.13: 7 residues within 4Å: Chain A: S.126, N.155, Y.161, E.163 Chain B: I.252, N.253, Y.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.126, A:N.155, A:E.163 Water bridges: A:S.126 EPE.27: 7 residues within 4Å: Chain A: I.252, N.253, Y.300 Chain B: S.126, N.155, Y.161, E.163 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.126, B:N.155 Water bridges: B:S.126

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

EDO.14: 2 residues within 4Å: Chain A: L.92, Q.94 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.93 EDO.28: 2 residues within 4Å: Chain B: L.92, Q.94 1 PLIP interactions: 1 interactions with chain B Water bridges: B:I.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicoludis, J.M. et al., Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4. Elife (2016)

Release Date

2016-08-24

Peptides

Protocadherin gamma-B3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protocadherin gamma-B3