SMTL ID : 6vfu.1 (1 other biounit)

Crystal structure of human protocadherin 19 EC1-EC4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-dimer

Ligands

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.1: 4 residues within 4Å: Chain A: N.399, T.401, S.417, T.419 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 6 residues within 4Å: Chain B: L.368, G.369, N.399, T.401, S.417, T.419 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.368 Hydrogen bonds: B:N.399, B:S.417

18 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: E.10, E.11, D.67, D.69, D.103, N.104 Ligands: CA.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.10, A:E.11, A:D.67, A:D.69, A:D.103 CA.4: 8 residues within 4Å: Chain A: E.10, D.69, D.100, L.101, D.103, N.104, D.136 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.10, A:D.69, A:L.101, A:D.103, A:D.136 CA.5: 9 residues within 4Å: Chain A: N.102, N.104, A.105, P.106, D.134, D.136, F.140, G.141, D.191 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.104, A:D.134, A:D.136, A:F.140, A:D.191 CA.6: 6 residues within 4Å: Chain A: E.119, D.176, E.178, D.212, N.213 Ligands: CA.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.119, A:D.176, A:E.178, A:D.212, H2O.1 CA.7: 9 residues within 4Å: Chain A: E.119, R.177, E.178, D.209, S.210, D.212, N.213, D.245 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.119, A:E.178, A:E.178, A:S.210, A:D.245 CA.8: 9 residues within 4Å: Chain A: N.211, N.213, N.214, P.215, D.243, D.245, N.249, G.250, D.299 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.213, A:D.243, A:D.245, A:N.249, A:D.299 CA.9: 9 residues within 4Å: Chain A: E.228, Y.285, E.286, D.317, T.318, D.320, N.321, D.356 Ligands: CA.10 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.228, A:D.317, A:T.318, A:D.320, A:D.356 CA.10: 7 residues within 4Å: Chain A: E.228, N.229, D.284, E.286, D.320, N.321 Ligands: CA.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.228, A:D.284, A:E.286, A:D.320 CA.11: 9 residues within 4Å: Chain A: N.319, N.321, P.323, D.354, D.356, N.360, G.361, D.406, L.412 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.321, A:D.354, A:D.356, A:N.360, A:D.406 CA.16: 7 residues within 4Å: Chain B: E.10, E.11, D.67, D.69, D.103, N.104 Ligands: CA.18 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.10, B:E.11, B:D.67, B:D.69, B:D.103 CA.17: 9 residues within 4Å: Chain B: N.102, N.104, A.105, P.106, D.134, D.136, F.140, G.141, D.191 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.104, B:D.134, B:D.136, B:F.140, B:D.191 CA.18: 8 residues within 4Å: Chain B: E.10, D.69, D.100, L.101, D.103, N.104, D.136 Ligands: CA.16 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.10, B:D.69, B:L.101, B:D.103, B:D.136 CA.19: 9 residues within 4Å: Chain B: E.119, R.177, E.178, D.209, S.210, D.212, N.213, D.245 Ligands: CA.20 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.119, B:E.178, B:E.178, B:S.210, B:D.245 CA.20: 7 residues within 4Å: Chain B: E.119, D.176, R.177, E.178, D.212, N.213 Ligands: CA.19 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.119, B:D.176, B:E.178, B:D.212, H2O.1 CA.21: 9 residues within 4Å: Chain B: N.211, N.213, N.214, P.215, D.243, D.245, N.249, G.250, D.299 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.213, B:D.243, B:D.245, B:N.249, B:D.299 CA.22: 8 residues within 4Å: Chain B: E.228, E.286, D.317, T.318, D.320, N.321, D.356 Ligands: CA.23 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.228, B:E.286, B:D.317, B:T.318, B:D.356 CA.23: 7 residues within 4Å: Chain B: E.228, N.229, D.284, E.286, D.320, N.321 Ligands: CA.22 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.228, B:D.284, B:E.286, B:D.320 CA.24: 9 residues within 4Å: Chain B: N.319, N.321, P.323, D.354, D.356, N.360, G.361, D.406, L.412 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.321, B:D.354, B:D.356, B:N.360, B:D.406

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

NAG.12: 2 residues within 4Å: Chain A: R.238, N.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.238, A:R.238 NAG.25: 2 residues within 4Å: Chain B: R.238, N.240 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.238, B:N.240

2 x NI: NICKEL (II) ION(Non-covalent)

NI.13: 3 residues within 4Å: Chain A: E.336, H.426, H.428 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.336, A:H.428 NI.26: 3 residues within 4Å: Chain B: E.336, H.426, H.428 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.336, B:E.336, B:H.426, B:H.426

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 3 residues within 4Å: Chain A: E.246, G.247, T.248 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain A: N.150, E.151, F.153, G.154, E.172 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain B: V.17 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain B: Q.269 Ligand excluded by 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-19: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

Protocadherin-19

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