SMTL ID : 6vg4.1

Human protocadherin 10 ectodomain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

monomer

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: 3 residues within 4Å: Chain A: L.486, Q.525, N.540 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: 4 residues within 4Å: Chain A: Q.254, N.256, T.258 Ligands: TAM.21 No protein-ligand interaction detected (PLIP)

15 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: E.9, E.10, D.63, R.64, E.65, D.100, N.101 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, R.64, E.65, D.97, I.98, D.100, N.101, D.133 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.65, A:D.97, A:I.98, A:D.133 CA.5: 9 residues within 4Å: Chain A: N.99, N.101, P.102, 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: 5 residues within 4Å: Chain A: E.116, D.173, R.174, E.175, D.228 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: 7 residues within 4Å: Chain A: E.116, R.174, E.175, D.225, S.226, D.228, D.261 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:E.116, A:E.175, A:D.225, A:S.226, A:D.228, A:D.261 CA.8: 7 residues within 4Å: Chain A: N.227, N.229, D.259, D.261, N.265, G.266, 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: 6 residues within 4Å: Chain A: E.244, N.245, D.300, Y.301, E.302, D.336 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.244, A:D.300, A:E.302, A:D.336, H2O.1 CA.10: 7 residues within 4Å: Chain A: E.244, Y.301, E.302, D.333, A.334, D.336, D.369 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.302, 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.12: 6 residues within 4Å: Chain A: E.352, D.405, E.407, D.441, N.442 Ligands: CA.13 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.352, A:D.405, A:E.407, A:D.441, A:D.441 CA.13: 9 residues within 4Å: Chain A: E.352, R.406, E.407, D.438, V.439, D.441, N.442, D.474 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.352, A:D.438, A:V.439, A:D.441, A:D.474 CA.14: 9 residues within 4Å: Chain A: N.440, N.442, P.444, D.472, D.474, N.478, A.479, D.530, L.537 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.442, A:D.472, A:D.474, A:N.478, A:D.530 CA.15: 6 residues within 4Å: Chain A: E.457, N.458, D.515, Y.516, E.517, D.552 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.457, A:D.515, A:E.517, A:D.552 CA.16: 8 residues within 4Å: Chain A: E.457, E.517, D.549, Q.550, N.551, D.552, N.553, D.592 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.457, A:E.517, A:Q.550, A:D.552, A:D.592 CA.17: 10 residues within 4Å: Chain A: N.551, N.553, A.554, P.555, D.590, D.592, N.596, A.597, D.645, L.651 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.553, A:D.590, A:D.592, A:N.596, A:D.645

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

MAN.18: 5 residues within 4Å: Chain A: V.187, Q.212, R.213, T.214 Ligands: MAN.19 No protein-ligand interaction detected (PLIP) MAN.19: 6 residues within 4Å: Chain A: V.183, T.185, T.214, G.215, T.216 Ligands: MAN.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.214 MAN.20: 6 residues within 4Å: Chain A: E.642, R.644, P.650, L.651, S.652, T.654 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.652

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.21: 8 residues within 4Å: Chain A: T.258, D.259, P.260, D.261, G.266, E.267, V.268 Ligands: NAG-NAG-BMA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.259, A:E.267

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

CL.22: 4 residues within 4Å: Chain A: R.512, F.514, D.515, L.519 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.23: 3 residues within 4Å: Chain A: N.147, S.151, E.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.147

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protocadherin-10