SMTL ID : 6vft.2 (1 other biounit)

Crystal structure of human delta protocadherin 17 EC1-EC4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.71 Å

Oligo State

homo-dimer

Ligands

2 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: 6 residues within 4Å: Chain A: E.227, Y.231, I.246, D.247, L.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.3: 5 residues within 4Å: Chain B: E.227, Y.231, D.247, L.248, N.249 No protein-ligand interaction detected (PLIP)

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.2: 5 residues within 4Å: Chain A: N.422, T.424, T.438, S.440 Ligands: NAG.16 No protein-ligand interaction detected (PLIP)

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.4: 3 residues within 4Å: Chain B: V.426, N.436, T.438 No protein-ligand interaction detected (PLIP)

20 x CA: CALCIUM ION(Non-covalent)

CA.5: 7 residues within 4Å: Chain A: E.10, E.11, D.74, R.75, E.76, D.110 Ligands: CA.6 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.10, A:E.11, A:D.74, A:E.76, A:D.110, H2O.1 CA.6: 8 residues within 4Å: Chain A: E.10, E.76, D.107, I.108, D.110, N.111, D.143 Ligands: CA.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.10, A:E.76, A:D.107, A:I.108, A:D.143 CA.7: 8 residues within 4Å: Chain A: N.109, N.111, A.112, D.141, D.143, N.147, G.148, D.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.111, A:D.141, A:D.141, A:D.143, A:N.147 CA.8: 8 residues within 4Å: Chain A: N.220, N.222, D.252, D.254, N.258, G.259, D.308, I.314 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.222, A:D.252, A:D.254, A:N.258, A:D.308 CA.9: 9 residues within 4Å: Chain A: E.126, R.186, E.187, D.218, S.219, D.221, N.222, D.254 Ligands: CA.10 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.126, A:E.187, A:D.218, A:D.221, A:D.254 CA.10: 7 residues within 4Å: Chain A: E.126, D.185, R.186, E.187, D.221, N.222 Ligands: CA.9 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.126, A:D.185, A:E.187, A:D.221, A:D.221 CA.11: 8 residues within 4Å: Chain A: E.237, N.238, D.293, Y.294, E.295, D.329, N.330 Ligands: CA.13 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.237, A:D.293, A:E.295, A:D.329, H2O.1 CA.12: 8 residues within 4Å: Chain A: N.328, N.330, D.361, D.363, N.367, G.368, D.429, L.435 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.330, A:D.361, A:D.363, A:N.367, A:D.429 CA.13: 9 residues within 4Å: Chain A: E.237, Y.294, E.295, D.326, R.327, D.329, N.330, D.363 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.237, A:E.295, A:D.326, A:R.327, A:D.329 CA.17: 6 residues within 4Å: Chain A: D.247, L.248, N.249, Y.263, T.283, G.284 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.247, A:L.248, A:T.283 CA.18: 9 residues within 4Å: Chain B: N.109, N.111, A.112, D.141, D.143, N.147, G.148, D.200, R.206 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.111, B:D.141, B:D.141, B:N.147, B:D.200 CA.19: 8 residues within 4Å: Chain B: E.10, E.76, D.107, I.108, D.110, N.111, D.143 Ligands: CA.20 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.10, B:E.76, B:D.107, B:I.108, B:D.143 CA.20: 8 residues within 4Å: Chain B: E.10, E.11, D.74, R.75, E.76, D.110, N.111 Ligands: CA.19 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.10, B:E.11, B:D.74, B:E.76, B:D.110 CA.21: 8 residues within 4Å: Chain B: N.220, N.222, D.252, D.254, N.258, G.259, D.308, I.314 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.222, B:D.252, B:D.254, B:N.258, B:D.308 CA.22: 9 residues within 4Å: Chain B: E.126, R.186, E.187, D.218, S.219, D.221, N.222, D.254 Ligands: CA.23 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.126, B:E.187, B:D.218, B:D.221, B:D.254 CA.23: 7 residues within 4Å: Chain B: E.126, D.185, R.186, E.187, D.221, N.222 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.126, B:D.185, B:E.187, B:D.221, B:D.221 CA.24: 8 residues within 4Å: Chain B: E.237, Y.294, E.295, D.326, R.327, D.329, N.330, D.363 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.237, B:D.326, B:R.327, B:D.329, B:D.363 CA.25: 7 residues within 4Å: Chain B: E.237, N.238, D.293, Y.294, E.295, D.329, N.330 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.237, B:D.293, B:E.295, B:D.329, H2O.1 CA.26: 8 residues within 4Å: Chain B: N.328, N.330, D.361, D.363, N.367, G.368, D.429, L.435 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.330, B:D.361, B:D.363, B:N.367, B:D.429 CA.29: 5 residues within 4Å: Chain B: D.247, L.248, N.249, T.283, G.284 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.247, B:L.248, B:T.283

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

MAN.14: 4 residues within 4Å: Chain A: L.199, P.205, S.207, T.209 No protein-ligand interaction detected (PLIP) MAN.15: 5 residues within 4Å: Chain A: D.118, V.195, T.209, V.210, Q.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.209, A:Q.211 MAN.27: 4 residues within 4Å: Chain B: L.199, P.205, S.207, T.209 No protein-ligand interaction detected (PLIP) MAN.28: 6 residues within 4Å: Chain B: D.118, Q.119, V.195, T.209, V.210, Q.211 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.211, B:Q.211

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

NAG.16: 5 residues within 4Å: Chain A: R.373, V.426, R.428, N.436 Ligands: NAG-NAG-BMA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.428, A:R.428, A:N.436

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-17: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Protocadherin-17

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