SMTL ID : 6e6b.1

Crystal structure of the Protocadherin GammaB4 extracellular domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.52 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: 4 residues within 4Å: Chain A: I.460, Q.501, S.511, N.513 No protein-ligand interaction detected (PLIP)

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.2: 4 residues within 4Å: Chain B: L.185, P.191, L.192, N.193 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.192

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 3 residues within 4Å: Chain B: Q.501, S.511, N.513 No protein-ligand interaction detected (PLIP)

30 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: E.9, E.10, D.61, E.63, D.98 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.9, A:E.10, A:E.63, A:D.98 CA.5: 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.6: 8 residues within 4Å: Chain A: N.97, H.99, T.100, P.101, D.129, D.131, N.135, D.186 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.99, A:D.129 CA.7: 4 residues within 4Å: Chain A: E.114, D.171, E.173, D.207 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.114, A:D.171, A:D.207 CA.8: 7 residues within 4Å: Chain A: E.114, R.172, E.173, D.204, A.205, D.207, D.240 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.114, A:D.204, A:A.205, A:D.207, A:D.240 CA.9: 6 residues within 4Å: Chain A: N.206, N.208, D.238, D.240, N.244, D.291 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.208, A:D.238, A:D.240, A:N.244, A:D.291 CA.10: 4 residues within 4Å: Chain A: E.223, D.276, E.278, D.310 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.223, A:D.276, A:D.310 CA.11: 7 residues within 4Å: Chain A: E.223, E.278, D.307, E.308, D.310, N.311, D.343 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.223, A:E.278, A:D.307, A:D.343 CA.12: 6 residues within 4Å: Chain A: N.309, N.311, D.341, D.343, N.347, D.394 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.311, A:D.341, A:D.341, A:D.343, A:N.347 CA.13: 6 residues within 4Å: Chain A: E.326, D.379, E.381, D.415, N.416 Ligands: CA.14 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.326, A:D.379, A:E.381, A:D.415 CA.14: 7 residues within 4Å: Chain A: E.326, E.381, D.412, V.413, D.415, D.448 Ligands: CA.13 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.326, A:E.381, A:D.412, A:V.413 CA.15: 6 residues within 4Å: Chain A: N.414, N.416, D.446, D.448, N.452, D.504 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.416, A:D.446, A:D.448, A:N.452, A:D.504 CA.16: 5 residues within 4Å: Chain A: E.431, D.489, E.491, D.525, N.526 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.431, A:D.489, A:E.491, A:D.525 CA.17: 6 residues within 4Å: Chain A: E.431, E.491, D.522, R.523, D.525, D.565 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.431, A:D.522, A:R.523, A:D.525, A:D.565 CA.18: 6 residues within 4Å: Chain A: N.524, N.526, D.563, D.565, N.569, D.616 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.526, A:D.563, A:D.563, A:N.569, A:D.616 CA.23: 6 residues within 4Å: Chain B: E.9, E.10, D.61, E.63, D.98, H.99 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.10, B:D.61, B:E.63, B:D.98 CA.24: 7 residues within 4Å: Chain B: E.9, E.63, D.95, I.96, D.98, H.99, 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.25: 6 residues within 4Å: Chain B: N.97, H.99, D.129, D.131, N.135, D.186 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.99, B:D.129, B:D.129, B:D.131, B:N.135 CA.26: 4 residues within 4Å: Chain B: E.114, D.171, E.173, D.207 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.114, B:D.171, B:D.207 CA.27: 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:D.207, B:D.240 CA.28: 6 residues within 4Å: Chain B: N.206, N.208, D.238, D.240, N.244, D.291 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.208, B:D.238, B:D.240, B:N.244, B:D.291 CA.29: 4 residues within 4Å: Chain B: E.223, D.276, E.278, D.310 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.276, B:D.310 CA.30: 7 residues within 4Å: Chain B: E.223, E.278, D.307, E.308, D.310, N.311, D.343 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.278, B:D.307, B:E.308, B:D.310, B:D.343 CA.31: 6 residues within 4Å: Chain B: N.309, N.311, D.341, D.343, N.347, D.394 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.311, B:D.341, B:D.343, B:N.347, B:D.394 CA.32: 6 residues within 4Å: Chain B: E.326, D.379, E.381, D.415, N.416 Ligands: CA.33 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.326, B:D.379, B:E.381, B:D.415 CA.33: 9 residues within 4Å: Chain B: E.326, R.380, E.381, D.412, V.413, D.415, N.416, D.448 Ligands: CA.32 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.326, B:E.381, B:D.412 CA.34: 6 residues within 4Å: Chain B: N.414, N.416, D.446, D.448, N.452, D.504 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.448, B:N.452, B:D.504 CA.35: 4 residues within 4Å: Chain B: E.431, D.489, E.491, D.525 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.431, B:D.489, B:D.525 CA.36: 7 residues within 4Å: Chain B: E.431, H.490, E.491, D.522, R.523, D.525, D.565 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.431, B:E.491, B:D.522 CA.37: 6 residues within 4Å: Chain B: N.524, N.526, D.563, D.565, N.569, D.616 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.526, B:D.563, B:D.565, B:N.569, B:D.616

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

MAN.19: 4 residues within 4Å: Chain A: R.615, P.621, S.623, T.625 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.615, A:R.615 MAN.20: 4 residues within 4Å: Chain A: S.438, I.439, A.440, Q.441 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.441 MAN.38: 2 residues within 4Å: Chain B: P.621, S.623 No protein-ligand interaction detected (PLIP) MAN.40: 4 residues within 4Å: Chain B: S.438, A.440, Q.441, V.481 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.441

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

NAG.21: 1 residues within 4Å: Chain A: N.387 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.387 NAG.22: 2 residues within 4Å: Chain A: T.183, N.193 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.183 Hydrogen bonds: A:N.193 NAG.39: 2 residues within 4Å: Chain B: E.385, N.387 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brasch, J. et al., Visualization of clustered protocadherin neuronal self-recognition complexes. Nature (2019)

Release Date

2019-04-10

Peptides

Protocadherin gamma B4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protocadherin gamma B4