SMTL ID : 5szl.2 (1 other biounit)

Protocadherin gamma A1 extracellular cadherin domains 1-4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.20 Å

Oligo State

homo-dimer

Ligands

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.1: 1 residues within 4Å: Chain A: N.237 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- FUC: 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-FUC.2: 2 residues within 4Å: Chain B: T.215, N.237 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.215

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

MAN.3: 2 residues within 4Å: Chain A: S.187, S.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.187 MAN.4: 2 residues within 4Å: Chain A: T.197, Q.199 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.199 MAN.15: 3 residues within 4Å: Chain B: T.197, Q.199 Ligands: MAN.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.199 MAN.16: 3 residues within 4Å: Chain B: I.193, S.195 Ligands: MAN.15 No protein-ligand interaction detected (PLIP)

18 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: N.208, N.210, D.240, D.242, N.246, D.295 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.210, A:D.240, A:D.242, A:N.246, A:D.295 CA.6: 6 residues within 4Å: Chain A: E.116, E.175, D.206, V.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:V.207, A:D.242 CA.7: 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.8: 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:D.97, A:I.98, A:D.100, A:D.133 CA.9: 6 residues within 4Å: Chain A: N.99, N.101, D.131, D.133, N.137, D.188 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.101, A:D.131, A:D.133, A:N.137, A:D.188 CA.10: 5 residues within 4Å: Chain A: E.9, E.10, D.63, E.65, D.100 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.11: 7 residues within 4Å: Chain A: E.225, E.282, D.311, V.312, D.314, D.347 Ligands: CA.12 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:E.225, A:E.282, A:D.311, A:V.312, A:D.314, A:D.347 CA.12: 6 residues within 4Å: Chain A: E.225, D.280, E.282, D.314, N.315 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.225, A:D.280, A:E.282, A:E.282, A:D.314 CA.13: 6 residues within 4Å: Chain A: N.313, N.315, D.345, D.347, N.351, D.398 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.315, A:D.345, A:D.347, A:N.351, A:D.398 CA.17: 6 residues within 4Å: Chain B: N.99, N.101, D.131, D.133, N.137, D.188 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.101, B:D.131, B:D.133, B:N.137, B:D.188 CA.18: 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.65, B:D.97, B:I.98, B:D.100, B:D.133 CA.19: 5 residues within 4Å: Chain B: E.9, E.10, D.63, E.65, D.100 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.20: 6 residues within 4Å: Chain B: N.208, N.210, D.240, D.242, N.246, D.295 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.210, B:D.240, B:D.242, B:N.246, B:D.295 CA.21: 6 residues within 4Å: Chain B: E.116, E.175, D.206, V.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:V.207, B:D.242 CA.22: 4 residues within 4Å: Chain B: E.116, D.173, E.175, D.209 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.116, B:D.173, B:E.175, B:D.209 CA.23: 5 residues within 4Å: Chain B: E.225, D.311, V.312, D.314, D.347 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.311, B:V.312, B:D.314, B:D.347 CA.24: 5 residues within 4Å: Chain B: E.225, D.280, F.281, E.282, D.314 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.225, B:D.280, B:E.282, B:D.314 CA.25: 6 residues within 4Å: Chain B: N.313, N.315, D.345, D.347, N.351, D.398 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.315, B:D.345, B:D.347, B:N.351, B:D.398

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

NAG.14: 1 residues within 4Å: Chain A: N.391 No protein-ligand interaction detected (PLIP) NAG.26: 1 residues within 4Å: Chain B: N.391 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.391

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goodman, K.M. et al., gamma-Protocadherin structural diversity and functional implications. Elife (2016)

Release Date

2016-10-19

Peptides

PROTOCADHERIN GAMMA A1 EXTRACELLULAR CADHERIN DOMAINS 1-4, Protein Pcdhga1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

PROTOCADHERIN GAMMA A1 EXTRACELLULAR CADHERIN DOMAINS 1-4, Protein Pcdhga1

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