SMTL ID : 5szn.1

Protocadherin gamma A9 extracellular cadherin domains 1-5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.94 Å

Oligo State

monomer

Ligands

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.1: 2 residues within 4Å: Chain A: E.389, N.391 No protein-ligand interaction detected (PLIP)

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

MAN.2: 3 residues within 4Å: Chain A: Y.187, R.193, S.195 No protein-ligand interaction detected (PLIP) MAN.3: 3 residues within 4Å: Chain A: E.108, T.197, L.199 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.108 MAN.4: 4 residues within 4Å: Chain A: S.442, F.444, S.445, V.485 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.444

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

NAG.5: 1 residues within 4Å: Chain A: N.517 No protein-ligand interaction detected (PLIP)

15 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: E.116, D.173, E.175, D.209, N.210 Ligands: CA.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.116, A:D.173, A:E.175, A:D.209 CA.7: 9 residues within 4Å: Chain A: E.116, R.174, E.175, D.206, T.207, D.209, N.210, D.242 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.116, A:E.175, A:D.206, A:D.209, A:D.242 CA.8: 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.9: 6 residues within 4Å: Chain A: E.225, D.280, E.282, D.314, N.315 Ligands: CA.10 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.225, A:D.280, A:E.282, A:D.314, A:D.314 CA.10: 8 residues within 4Å: Chain A: E.225, E.282, D.311, V.312, D.314, N.315, D.347 Ligands: CA.9 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.225, A:E.282, A:D.311, A:D.314, A:D.347 CA.11: 8 residues within 4Å: Chain A: E.330, R.384, E.385, D.416, I.417, D.419, D.452 Ligands: CA.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.385, A:D.416, A:I.417, A:D.452 CA.12: 6 residues within 4Å: Chain A: E.330, D.383, E.385, D.419, N.420 Ligands: CA.11 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.330, A:E.330, A:E.385, A:D.419, H2O.1 CA.13: 6 residues within 4Å: Chain A: N.418, N.420, D.450, D.452, N.456, D.508 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.420, A:D.450, A:D.452, A:N.456, A:D.508 CA.14: 7 residues within 4Å: Chain A: E.9, E.10, D.63, E.65, D.100, N.101 Ligands: CA.15 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:D.63, A:E.65, A:D.100, A:D.100 CA.15: 7 residues within 4Å: Chain A: E.9, E.65, D.97, I.98, D.100, D.133 Ligands: CA.14 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.65, A:I.98, A:D.100, A:D.133 CA.16: 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.131, A:N.137, A:D.188 CA.17: 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.345, A:D.347, A:N.351 CA.18: 6 residues within 4Å: Chain A: E.435, D.493, E.495, D.526, D.529 Ligands: CA.19 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.435, A:E.435, A:E.495, A:D.529, A:D.529 CA.19: 4 residues within 4Å: Chain A: E.435, D.493, D.529 Ligands: CA.18 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.435, A:D.493 CA.20: 2 residues within 4Å: Chain A: S.326, T.411 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 4 residues within 4Å: Chain A: F.253, F.264, H.265, L.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.266 GOL.22: 3 residues within 4Å: Chain A: K.222, L.224, E.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.222 Water bridges: A:K.222, A:K.222, A:L.224

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 A9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protocadherin gamma A9