SMTL ID : 5dzw.1

Protocadherin alpha 4 extracellular cadherin domains 1-4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

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

MAN.1: 2 residues within 4Å: Chain A: T.409, A.410 No protein-ligand interaction detected (PLIP) MAN.2: 4 residues within 4Å: Chain A: K.393, S.411, S.413 Ligands: MAN.3 No protein-ligand interaction detected (PLIP) MAN.3: 6 residues within 4Å: Chain A: D.391, Y.392, K.393, S.413, E.415 Ligands: MAN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.391, A:E.415 MAN.14: 2 residues within 4Å: Chain B: T.409, A.410 No protein-ligand interaction detected (PLIP) MAN.15: 4 residues within 4Å: Chain B: K.393, S.411, S.413 Ligands: MAN.16 No protein-ligand interaction detected (PLIP) MAN.16: 6 residues within 4Å: Chain B: D.391, Y.392, K.393, S.413, E.415 Ligands: MAN.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.391, B:E.415, B:E.415

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

NAG.4: 3 residues within 4Å: Chain A: D.214, N.236, S.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.214, A:N.236 NAG.17: 3 residues within 4Å: Chain B: D.214, N.236, S.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.214, B:N.236

18 x CA: CALCIUM ION(Non-covalent)

CA.5: 7 residues within 4Å: Chain A: E.8, E.64, D.96, I.97, D.99, D.132 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.8, A:E.64, A:D.96, A:I.97, A:D.99 CA.6: 6 residues within 4Å: Chain A: E.8, E.9, D.62, E.64, D.99 Ligands: CA.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.8, A:E.64, A:E.64, A:D.99, A:D.99 CA.7: 6 residues within 4Å: Chain A: N.98, N.100, D.130, D.132, N.136, D.187 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:N.100, A:D.130, A:D.132, A:N.136 CA.8: 7 residues within 4Å: Chain A: E.115, E.174, D.205, A.206, D.208, D.241 Ligands: CA.9 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.174, A:D.205, A:A.206, A:D.208, A:D.241 CA.9: 6 residues within 4Å: Chain A: E.115, D.172, E.174, D.208, N.209 Ligands: CA.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.115, A:E.174, A:D.208, A:D.208 CA.10: 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.11: 7 residues within 4Å: Chain A: E.224, D.280, E.282, D.316, N.317, D.349 Ligands: CA.12 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.12: 8 residues within 4Å: Chain A: E.224, E.282, D.313, I.314, D.316, N.317, D.349 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.224, A:E.282, A:D.313, A:I.314, A:D.349 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.18: 7 residues within 4Å: Chain B: E.8, E.64, D.96, I.97, D.99, D.132 Ligands: CA.19 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.8, B:E.64, B:D.96, B:I.97, B:D.99 CA.19: 6 residues within 4Å: Chain B: E.8, E.9, D.62, E.64, D.99 Ligands: CA.18 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.8, B:E.64, B:E.64, B:D.99, B:D.99 CA.20: 6 residues within 4Å: Chain B: N.98, N.100, D.130, D.132, N.136, D.187 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:N.100, B:D.130, B:D.132, B:N.136 CA.21: 7 residues within 4Å: Chain B: E.115, E.174, D.205, A.206, D.208, D.241 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.174, B:D.205, B:A.206, B:D.208, B:D.241 CA.22: 6 residues within 4Å: Chain B: E.115, D.172, E.174, D.208, N.209 Ligands: CA.21 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.115, B:E.174, B:D.208, B:D.208 CA.23: 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.241, B:N.245, B:D.295 CA.24: 7 residues within 4Å: Chain B: E.224, D.280, E.282, D.316, N.317, D.349 Ligands: CA.25 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.224, B:D.280, B:E.282, B:D.316, B:D.316 CA.25: 8 residues within 4Å: Chain B: E.224, E.282, D.313, I.314, D.316, N.317, D.349 Ligands: CA.24 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.224, B:E.282, B:D.313, B:I.314, B:D.349 CA.26: 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:N.317, B:D.347, B:D.349, B:N.353, B:D.400

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 alpha-4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protocadherin alpha-4