SMTL ID : 5dzv.1

Protocadherin alpha 7 extracellular cadherin domains 1-5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

homo-dimer

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 2 residues within 4Å: Chain A: D.214, N.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.236 NAG-FUC.2: 2 residues within 4Å: Chain A: N.228, I.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.276

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[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-MAN-FUC.3: 4 residues within 4Å: Chain B: N.228, G.229, H.265, I.276 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.228, B:H.265

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 2 residues within 4Å: Chain B: N.236, Y.250 No protein-ligand interaction detected (PLIP)

24 x CA: CALCIUM ION(Non-covalent)

CA.5: 7 residues within 4Å: Chain A: E.8, E.64, D.96, I.97, D.99, N.100, D.132 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:E.8, A:E.64, A:D.96, A:I.97, A:D.99, A:D.132 CA.6: 6 residues within 4Å: Chain A: N.98, N.100, D.130, D.132, N.136, D.187 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.130, A:D.130, A:D.132, A:N.136, A:D.187 CA.7: 6 residues within 4Å: Chain A: E.8, E.9, D.62, E.64, D.99, N.100 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.8, A:E.9, A:D.62, A:E.64, A:D.99 CA.8: 8 residues within 4Å: Chain A: E.115, E.174, D.205, V.206, D.208, N.209, D.241 Ligands: CA.10 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.115, A:E.174, A:D.205, A:V.206, A:D.241 CA.9: 6 residues within 4Å: Chain A: N.207, N.209, D.239, D.241, N.245, D.295 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.209, A:D.239, A:D.241, A:N.245, A:D.295 CA.10: 6 residues within 4Å: Chain A: E.115, D.172, E.174, D.208, N.209 Ligands: CA.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.115, A:D.172, A:D.208 CA.11: 8 residues within 4Å: Chain A: E.224, F.281, E.282, D.313, A.314, D.316, D.349 Ligands: CA.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.224, A:E.224, A:E.282, A:D.313 CA.12: 6 residues within 4Å: Chain A: E.224, D.280, E.282, D.316, N.317 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.224, A:D.280, A:E.282, A:D.316, A:D.316 CA.13: 6 residues within 4Å: Chain A: N.315, N.317, D.347, D.349, N.353, D.400 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.317, A:D.347, A:D.349, A:N.353, A:D.400 CA.14: 8 residues within 4Å: Chain A: E.332, R.386, E.387, D.418, V.419, D.421, D.454 Ligands: CA.15 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.332, A:E.387, A:D.418, A:V.419 CA.15: 6 residues within 4Å: Chain A: E.332, D.385, E.387, D.421, N.422 Ligands: CA.14 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.332, A:E.332, A:E.387, A:D.421, A:D.421 CA.16: 6 residues within 4Å: Chain A: N.420, N.422, D.452, D.454, N.458, D.510 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.452, A:D.454, A:N.458 CA.19: 7 residues within 4Å: Chain B: E.8, E.64, D.96, I.97, D.99, D.132 Ligands: CA.20 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.8, B:D.96, B:I.97, B:D.99, B:D.132 CA.20: 6 residues within 4Å: Chain B: E.8, E.9, D.62, E.64, D.99 Ligands: CA.19 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.8, B:E.64, B:D.99, B:D.99 CA.21: 6 residues within 4Å: Chain B: N.98, N.100, D.130, D.132, N.136, D.187 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.130, B:D.130, B:D.132, B:N.136, B:D.187 CA.22: 8 residues within 4Å: Chain B: E.115, E.174, D.205, V.206, D.208, N.209, D.241 Ligands: CA.23 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.115, B:E.174, B:D.205, B:D.208, B:D.241 CA.23: 6 residues within 4Å: Chain B: E.115, D.172, E.174, D.208, N.209 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.115, B:D.172, B:E.174, B:D.208, B:D.208 CA.24: 6 residues within 4Å: Chain B: N.207, N.209, D.239, D.241, N.245, D.295 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.209, B:D.239, B:D.239, B:D.241, B:N.245 CA.25: 7 residues within 4Å: Chain B: E.224, E.282, D.313, A.314, D.316, D.349 Ligands: CA.26 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.224, B:E.224, B:E.282, B:D.313, B:D.349 CA.26: 6 residues within 4Å: Chain B: E.224, D.280, E.282, D.316, N.317 Ligands: CA.25 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.224, B:D.280, B:E.282, B:D.316 CA.27: 6 residues within 4Å: Chain B: N.315, N.317, D.347, D.349, N.353, D.400 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.347, B:D.347, B:D.349, B:N.353, B:D.400 CA.28: 8 residues within 4Å: Chain B: E.332, E.387, D.418, V.419, D.421, N.422, D.454 Ligands: CA.29 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.332, B:E.387, B:D.418, B:V.419, B:D.454 CA.29: 6 residues within 4Å: Chain B: E.332, D.385, E.387, D.421, N.422 Ligands: CA.28 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.332, B:D.385, B:E.387, B:D.421, B:D.421 CA.30: 6 residues within 4Å: Chain B: N.420, N.422, D.452, D.454, N.458, D.510 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.422, B:D.452, B:D.454, B:N.458, B:D.510

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

MAN.17: 2 residues within 4Å: Chain A: T.196, Q.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.198 MAN.18: 2 residues within 4Å: Chain A: E.192, T.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.192 MAN.31: 3 residues within 4Å: Chain B: T.107, T.196, Q.198 No protein-ligand interaction detected (PLIP) MAN.32: 5 residues within 4Å: Chain B: T.184, T.186, E.192, L.193, T.194 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.192 MAN.34: 3 residues within 4Å: Chain B: I.395, T.409, S.411 No protein-ligand interaction detected (PLIP) MAN.35: 2 residues within 4Å: Chain B: S.449, M.451 No protein-ligand interaction detected (PLIP)

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

NAG.33: 1 residues within 4Å: Chain B: N.519 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.519

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

Protein Pcdha7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein Pcdha7