SMTL ID : 6mer.1

PcdhgB3 EC1-4 in 50 mM HEPES

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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, N.99 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: 6 residues within 4Å: Chain A: E.9, E.63, D.95, I.96, D.98, D.131 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.63, A:D.95, A:I.96, 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:D.309, A:E.310, A:D.312, 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: 5 residues within 4Å: Chain A: E.114, D.171, E.173, D.207, N.208 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.114, A:D.171, A:E.173, A:D.207 CA.9: 6 residues within 4Å: Chain A: E.114, E.173, D.204, A.205, D.207, D.240 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.114, A:E.173, A:D.204, A:A.205, A:D.240 CA.10: 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.11: 6 residues within 4Å: Chain B: E.9, E.10, D.61, E.63, D.98, N.99 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.12: 6 residues within 4Å: Chain B: E.9, E.63, D.95, I.96, D.98, D.131 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.63, B:D.95, B:I.96, B:D.131 CA.13: 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.14: 8 residues within 4Å: Chain B: E.223, E.280, D.309, E.310, D.312, N.313, D.345 Ligands: CA.15 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.223, B:D.309, B:E.310, B:D.312, B:D.345 CA.15: 6 residues within 4Å: Chain B: E.223, D.278, E.280, D.312, N.313 Ligands: CA.14 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.16: 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.17: 5 residues within 4Å: Chain B: E.114, D.171, E.173, D.207, N.208 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.114, B:D.171, B:E.173, B:D.207 CA.18: 6 residues within 4Å: Chain B: E.114, E.173, D.204, A.205, D.207, D.240 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.114, B:E.173, B:D.204, B:A.205, B:D.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicoludis, J.M. et al., Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-09-04

Peptides

Protocadherin gamma-B3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protocadherin gamma-B3

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