SMTL ID : 6vft.1 (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- 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.1: 7 residues within 4Å: Chain A: E.227, Y.231, I.246, D.247, L.248, N.249 Ligands: CA.16 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.2: 7 residues within 4Å: Chain A: L.375, N.422, T.424, T.438, K.439, S.440, A.442 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.422, A:T.438

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.3: 2 residues within 4Å: Chain A: L.435, N.436 No protein-ligand interaction detected (PLIP)

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

20 x CA: CALCIUM ION(Non-covalent)

CA.5: 8 residues within 4Å: Chain A: E.10, E.11, D.74, R.75, E.76, D.110, N.111 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.10, A:E.11, A:D.74, A:E.76, A:D.110 CA.6: 9 residues within 4Å: Chain A: E.10, R.75, 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: 9 residues within 4Å: Chain A: 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 A Metal complexes: A:N.111, A:D.141, A:D.143, A:N.147, A:D.200 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: 7 residues within 4Å: Chain A: E.237, N.238, D.293, Y.294, E.295, D.329, N.330 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.237, A:D.293, A:E.295, A:D.329 CA.10: 8 residues within 4Å: Chain A: E.237, Y.294, E.295, D.326, R.327, D.329, N.330, D.363 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.237, A:D.326, A:R.327, A:D.329, A:D.363 CA.11: 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.12: 7 residues within 4Å: Chain A: E.126, D.185, R.186, E.187, D.221, N.222 Ligands: CA.13 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.126, A:D.185, A:E.187, A:D.221, H2O.1 CA.13: 9 residues within 4Å: Chain A: E.126, R.186, E.187, D.218, S.219, D.221, N.222, D.254 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.126, A:E.187, A:E.187, A:D.221, A:D.254 CA.16: 6 residues within 4Å: Chain A: D.247, L.248, N.249, T.283, G.284 Ligands: NAG-NAG-FUC.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.247, A:L.248, A:T.283 CA.17: 8 residues within 4Å: Chain B: E.10, E.11, D.74, R.75, E.76, D.110, N.111 Ligands: CA.18 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.18: 9 residues within 4Å: Chain B: E.10, R.75, E.76, D.107, I.108, D.110, N.111, D.143 Ligands: CA.17 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.19: 10 residues within 4Å: Chain B: N.109, N.111, A.112, P.113, 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.143, B:N.147, B:D.200 CA.20: 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.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.20 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.126, B:D.218, B:S.219, B:D.221, B:D.254 CA.23: 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.24: 7 residues within 4Å: Chain B: E.237, N.238, D.293, Y.294, E.295, D.329, N.330 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.237, B:D.293, B:E.295, B:D.329 CA.25: 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.30: 4 residues within 4Å: Chain B: D.247, L.248, N.249, T.283 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: 5 residues within 4Å: Chain A: D.118, V.195, T.209, V.210, Q.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.211 MAN.15: 5 residues within 4Å: Chain A: T.197, L.199, P.205, S.207, T.209 No protein-ligand interaction detected (PLIP) MAN.26: 7 residues within 4Å: Chain B: T.197, L.199, P.205, S.207, A.208, T.209 Ligands: MAN.27 No protein-ligand interaction detected (PLIP) MAN.27: 7 residues within 4Å: Chain B: D.118, V.195, T.197, T.209, V.210, Q.211 Ligands: MAN.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.118, B:Q.211

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

NAG.28: 5 residues within 4Å: Chain B: R.373, V.426, R.428, N.436, T.438 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.428 NAG.29: 3 residues within 4Å: Chain B: N.422, T.424, S.440 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.422, B:S.440

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
A

B
C

Protocadherin-17

Related Entries With Identical Sequence