SMTL ID : 5dzx.1

Protocadherin beta 6 extracellular cadherin domains 1-4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.1: 3 residues within 4Å: Chain A: N.141, T.143 Ligands: MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.2: 3 residues within 4Å: Chain A: N.389, T.391, Q.405 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.357, A:Q.405

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 2 residues within 4Å: Chain B: N.141, T.143 No protein-ligand interaction detected (PLIP)

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

MAN.4: 3 residues within 4Å: Chain A: L.187, S.195 Ligands: NAG-NAG-BMA-MAN-FUC.1 No protein-ligand interaction detected (PLIP) MAN.14: 1 residues within 4Å: Chain B: S.195 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.195 MAN.15: 1 residues within 4Å: Chain B: T.197 No protein-ligand interaction detected (PLIP)

18 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: E.9, E.10, D.63, E.65, D.100, H.101 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.10, A:D.63, A:E.65, A:D.100 CA.6: 6 residues within 4Å: Chain A: E.9, E.65, D.97, I.98, D.100, D.133 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.65, A:D.97, A:I.98, A:D.133 CA.7: 6 residues within 4Å: Chain A: N.99, H.101, D.131, D.133, N.137, D.188 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.101, A:D.131, A:D.133, A:N.137, A:D.188 CA.8: 5 residues within 4Å: Chain A: E.116, D.173, E.175, D.209, N.210 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.116, A:D.173, A:E.175, A:D.209 CA.9: 6 residues within 4Å: Chain A: E.116, E.175, D.206, I.207, D.209, D.242 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.116, A:E.175, A:D.206, A:I.207, A:D.242 CA.10: 6 residues within 4Å: Chain A: N.208, N.210, D.240, D.242, H.246, D.294 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.240, A:D.240, A:D.242, A:H.246, A:D.294 CA.11: 6 residues within 4Å: Chain A: E.225, D.279, E.281, D.313, N.314 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.225, A:E.225, A:D.279, A:E.281, A:D.313 CA.12: 7 residues within 4Å: Chain A: E.225, E.281, D.310, V.311, D.313, D.345 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.225, A:E.281, A:D.310, A:V.311, A:D.313 CA.13: 6 residues within 4Å: Chain A: N.312, N.314, D.343, D.345, N.349, D.396 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.314, A:D.343, A:D.345, A:N.349, A:D.396 CA.16: 6 residues within 4Å: Chain B: E.9, E.10, D.63, E.65, D.100, H.101 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.10, B:D.63, B:E.65, B:D.100 CA.17: 6 residues within 4Å: Chain B: E.9, E.65, D.97, I.98, D.100, D.133 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.65, B:D.97, B:I.98, B:D.133 CA.18: 6 residues within 4Å: Chain B: N.99, H.101, D.131, D.133, N.137, D.188 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.101, B:D.131, B:D.133, B:N.137, B:D.188 CA.19: 5 residues within 4Å: Chain B: E.116, D.173, E.175, D.209, N.210 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.116, B:D.173, B:E.175, B:D.209 CA.20: 7 residues within 4Å: Chain B: E.116, R.174, E.175, D.206, I.207, D.209, D.242 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.116, B:E.175, B:D.206, B:D.209, B:D.242 CA.21: 6 residues within 4Å: Chain B: N.208, N.210, D.240, D.242, H.246, D.294 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.210, B:D.240, B:D.242, B:H.246, B:D.294 CA.22: 5 residues within 4Å: Chain B: E.225, D.279, E.281, D.313 Ligands: CA.23 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.225, B:E.225, B:D.279, B:E.281, B:D.313 CA.23: 7 residues within 4Å: Chain B: E.225, E.281, D.310, V.311, D.313, D.345 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.225, B:E.281, B:D.310, B:V.311, B:D.313 CA.24: 6 residues within 4Å: Chain B: N.312, N.314, D.343, D.345, N.349, D.396 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.314, B:D.343, B:D.345, B:N.349, B:D.396

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goodman, K.M. et al., Structural Basis of Diverse Homophilic Recognition by Clustered alpha- and beta-Protocadherins. Neuron (2016)

Release Date

2016-05-04

Peptides

Protocadherin beta 6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protocadherin beta 6