SMTL ID : 6vfw.2 (2 other biounits)

Crystal structure of human delta protocadherin 10 EC1-EC4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

homo-dimer

Ligands

2 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.1: 2 residues within 4Å: Chain A: N.256, T.258 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-FUC.2: 3 residues within 4Å: Chain B: Q.254, N.256, T.258 No protein-ligand interaction detected (PLIP)

18 x CA: CALCIUM ION(Non-covalent)

CA.3: 8 residues within 4Å: Chain A: E.9, E.10, D.63, R.64, E.65, D.100, N.101 Ligands: CA.4 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.4: 8 residues within 4Å: Chain A: E.9, E.65, D.97, I.98, D.100, N.101, D.133 Ligands: CA.3 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.5: 8 residues within 4Å: Chain A: N.99, N.101, P.103, D.131, D.133, N.137, S.138, 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.6: 7 residues within 4Å: Chain A: E.116, D.173, R.174, E.175, D.228, N.229 Ligands: CA.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.116, A:D.173, A:E.175, A:D.228, H2O.1 CA.7: 9 residues within 4Å: Chain A: E.116, R.174, E.175, D.225, S.226, D.228, N.229, D.261 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.116, A:D.225, A:S.226, A:D.228, A:D.261 CA.8: 6 residues within 4Å: Chain A: N.227, N.229, D.259, D.261, N.265, D.315 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.229, A:D.259, A:D.261, A:N.265, A:D.315 CA.9: 7 residues within 4Å: Chain A: E.244, N.245, D.300, Y.301, E.302, D.336, N.337 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.244, A:D.300, A:D.336, H2O.1, H2O.1 CA.10: 8 residues within 4Å: Chain A: E.244, E.302, D.333, A.334, N.335, D.336, N.337, D.369 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.244, A:D.333, A:A.334, A:D.336, A:D.369 CA.11: 8 residues within 4Å: Chain A: N.335, N.337, D.367, D.369, N.373, G.374, D.420, L.426 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.337, A:D.367, A:D.369, A:N.373, A:D.420 CA.14: 7 residues within 4Å: Chain B: E.9, E.10, D.63, R.64, E.65, D.100, N.101 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.15: 8 residues within 4Å: Chain B: E.9, R.64, E.65, D.97, I.98, D.100, N.101, D.133 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.65, B:D.97, B:I.98, B:D.133 CA.16: 8 residues within 4Å: Chain B: N.99, N.101, P.102, D.131, D.133, N.137, S.138, 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.17: 5 residues within 4Å: Chain B: E.116, D.173, E.175, D.228, N.229 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.116, B:D.173, B:E.175, B:D.228, H2O.1 CA.18: 8 residues within 4Å: Chain B: E.116, R.174, E.175, D.225, S.226, D.228, N.229, D.261 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.116, B:D.225, B:S.226, B:D.228, B:D.261 CA.19: 7 residues within 4Å: Chain B: N.227, N.229, P.231, D.259, D.261, N.265, D.315 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.229, B:D.259, B:D.261, B:N.265, B:D.315 CA.20: 7 residues within 4Å: Chain B: E.244, N.245, D.300, Y.301, E.302, D.336, N.337 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.244, B:D.300, B:E.302, B:D.336, H2O.1 CA.21: 9 residues within 4Å: Chain B: E.244, Y.301, E.302, D.333, A.334, N.335, D.336, N.337, D.369 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.244, B:D.333, B:A.334, B:D.336, B:D.369 CA.22: 10 residues within 4Å: Chain B: N.335, N.337, A.338, P.339, D.367, D.369, N.373, G.374, D.420, L.426 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.337, B:D.367, B:D.369, B:N.373, B:D.420

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

MAN.12: 5 residues within 4Å: Chain A: V.187, Q.212, R.213, T.214 Ligands: MAN.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.212 MAN.13: 6 residues within 4Å: Chain A: V.183, T.185, T.214, G.215, T.216 Ligands: MAN.12 No protein-ligand interaction detected (PLIP) MAN.23: 5 residues within 4Å: Chain B: V.187, Q.212, R.213, T.214 Ligands: MAN.24 No protein-ligand interaction detected (PLIP) MAN.24: 6 residues within 4Å: Chain B: V.183, T.185, T.214, G.215, T.216 Ligands: MAN.23 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harrison, O.J. et al., Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered delta-Protocadherins. Cell Rep (2020)

Release Date

2020-03-11

Peptides

Protocadherin-10: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Protocadherin-10

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