SMTL ID : 6vfq.1

Crystal structure of monomeric human protocadherin 10 EC1-EC4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

9 x CA: CALCIUM ION(Non-covalent)

CA.2: 8 residues within 4Å: Chain A: E.9, E.10, D.63, R.64, E.65, D.100, N.101 Ligands: CA.3 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.9, A:E.10, A:D.63, A:E.65, A:D.100, H2O.3 CA.3: 9 residues within 4Å: Chain A: E.9, R.64, E.65, D.97, I.98, D.100, N.101, D.133 Ligands: CA.2 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.4: 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.5: 7 residues within 4Å: Chain A: E.116, D.173, R.174, E.175, D.228, N.229 Ligands: CA.6 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.116, A:D.173, A:E.175, A:D.228, H2O.1, H2O.4 CA.6: 9 residues within 4Å: Chain A: E.116, R.174, E.175, D.225, S.226, D.228, N.229, D.261 Ligands: CA.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.116, A:E.175, A:S.226, A:D.228, A:D.261 CA.7: 8 residues within 4Å: Chain A: N.227, N.229, P.231, 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.8: 7 residues within 4Å: Chain A: E.244, D.300, Y.301, E.302, D.336, N.337 Ligands: CA.9 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.244, A:D.300, A:E.302, A:D.336, H2O.2, H2O.5 CA.9: 9 residues within 4Å: Chain A: E.244, Y.301, E.302, D.333, A.334, D.336, N.337, D.369 Ligands: CA.8 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.244, A:E.302, A:A.334, A:D.336, A:D.369 CA.10: 10 residues within 4Å: Chain A: 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 A Metal complexes: A:N.337, A:D.367, A:D.369, A:N.373, A:D.420

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

MAN.11: 6 residues within 4Å: Chain A: T.185, V.187, Q.212, R.213, T.214 Ligands: MAN.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.212, A:Q.212 MAN.12: 6 residues within 4Å: Chain A: V.183, T.185, T.214, G.215, T.216 Ligands: MAN.11 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 6 residues within 4Å: Chain A: D.259, P.260, D.261, E.262, G.266, E.267 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.259, A:D.259

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.14: 4 residues within 4Å: Chain A: L.381, T.415, V.417, S.429 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.429 EDO.15: 3 residues within 4Å: Chain A: S.364, T.366, Y.395 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.395 EDO.16: 10 residues within 4Å: Chain A: Q.70, D.131, P.132, D.133, V.134, G.135, S.138, D.159, G.160, N.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.131, A:G.135 EDO.17: 7 residues within 4Å: Chain A: N.147, S.148, Y.149, Q.177, H.180, R.181, Y.182 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.148, A:Q.177, A:H.180, A:Y.182

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

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