SMTL ID : 6vg1.1

xenopus protocadherin 8.1 EC1-6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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: 3 residues within 4Å: Chain A: E.396, N.398, Q.416 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.2: 3 residues within 4Å: Chain B: E.396, N.398, Q.416 No protein-ligand interaction detected (PLIP)

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

EDO.3: 9 residues within 4Å: Chain A: F.212, E.213, R.214, V.217, L.232, D.233, L.234, D.235, C.304 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.214 EDO.42: 4 residues within 4Å: Chain B: R.214, S.216, V.217, M.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.214 Water bridges: B:M.218

30 x CA: CALCIUM ION(Non-covalent)

CA.4: 8 residues within 4Å: Chain A: E.9, R.60, E.61, D.95, I.96, D.98, N.99, D.131 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.61, A:I.96, A:D.98, A:D.131 CA.5: 7 residues within 4Å: Chain A: E.9, E.10, D.59, R.60, E.61, I.96, D.98 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.10, A:D.59, A:E.61, A:D.98 CA.6: 9 residues within 4Å: Chain A: N.97, N.99, S.100, P.101, D.129, D.131, N.135, D.186, R.192 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.99, A:D.129, A:D.131, A:N.135, A:D.186 CA.7: 8 residues within 4Å: Chain A: E.114, R.172, E.173, D.204, F.205, D.207, D.240 Ligands: CA.9 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.114, A:E.173, A:E.173, A:F.205, A:D.240 CA.8: 10 residues within 4Å: Chain A: N.206, N.208, S.209, P.210, D.238, D.240, N.244, G.245, D.294, L.300 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.208, A:D.238, A:D.240, A:N.244, A:D.294 CA.9: 7 residues within 4Å: Chain A: E.114, D.171, R.172, E.173, D.207, N.208 Ligands: CA.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.114, A:D.171, A:D.207, H2O.1, H2O.2 CA.10: 6 residues within 4Å: Chain A: E.223, D.279, F.280, E.281, D.315, N.316 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.223, A:D.279, A:E.281, A:D.315, H2O.2, H2O.2 CA.11: 8 residues within 4Å: Chain A: E.223, F.280, E.281, D.312, V.313, D.315, N.316, D.354 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.223, A:E.281, A:E.281, A:D.312, A:D.354 CA.12: 9 residues within 4Å: Chain A: N.314, N.316, A.317, D.352, D.354, N.358, G.359, D.405, F.411 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.316, A:D.352, A:D.354, A:N.358, A:D.405 CA.13: 5 residues within 4Å: Chain A: E.337, D.390, R.391, E.392, D.426 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.337, A:D.390, A:E.392, A:D.426 CA.14: 8 residues within 4Å: Chain A: E.337, R.391, E.392, D.423, E.424, N.425, D.426, D.459 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.337, A:E.392, A:D.423, A:E.424, A:D.459 CA.15: 6 residues within 4Å: Chain A: E.442, E.502, D.533, Q.534, D.536, D.574 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.442, A:D.533, A:Q.534, A:D.536, A:D.574 CA.16: 6 residues within 4Å: Chain A: E.442, N.443, N.500, E.502, D.536 Ligands: CL.19 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.442, A:E.502, A:D.536, A:D.536 CA.17: 8 residues within 4Å: Chain A: N.535, N.537, A.538, P.539, D.572, D.574, N.578, D.624 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.537, A:D.572, A:D.574, A:N.578, A:D.624 CA.18: 8 residues within 4Å: Chain A: N.425, N.427, A.428, D.457, D.459, N.463, G.464, D.515 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.427, A:D.457, A:D.459, A:N.463, A:D.515 CA.23: 7 residues within 4Å: Chain B: E.9, E.61, D.95, I.96, D.98, D.131 Ligands: CA.24 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.61, B:D.95, B:D.98, B:D.131 CA.24: 8 residues within 4Å: Chain B: E.9, E.10, R.57, D.59, E.61, D.98, N.99 Ligands: CA.23 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.9, B:D.59, B:E.61, B:D.98, H2O.5 CA.25: 8 residues within 4Å: Chain B: N.97, N.99, S.100, P.101, D.129, D.131, N.135, D.186 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.99, B:D.129, B:D.131, B:N.135, B:D.186 CA.26: 7 residues within 4Å: Chain B: E.114, D.171, R.172, E.173, D.207, N.208 Ligands: CA.27 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.114, B:D.171, B:E.173, B:D.207 CA.27: 8 residues within 4Å: Chain B: E.114, R.172, E.173, D.204, F.205, D.207, D.240 Ligands: CA.26 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.114, B:E.173, B:D.204, B:F.205, B:D.240 CA.28: 9 residues within 4Å: Chain B: N.206, N.208, S.209, D.238, D.240, N.244, G.245, D.294, L.300 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.208, B:D.238, B:D.238, B:N.244, B:D.294 CA.29: 5 residues within 4Å: Chain B: E.223, D.279, F.280, E.281, D.315 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.223, B:D.279, B:E.281, B:D.315, H2O.5 CA.30: 7 residues within 4Å: Chain B: E.223, F.280, E.281, D.312, V.313, D.315, D.354 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.223, B:E.281, B:D.312, B:D.315, B:D.354 CA.31: 9 residues within 4Å: Chain B: N.314, N.316, A.317, D.352, D.354, N.358, G.359, D.405, F.411 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.316, B:D.352, B:D.354, B:N.358, B:D.405 CA.32: 5 residues within 4Å: Chain B: E.337, D.390, R.391, E.392, D.426 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.337, B:D.390, B:E.392, B:D.426, H2O.6 CA.33: 7 residues within 4Å: Chain B: E.337, R.391, E.392, D.423, E.424, D.426, D.459 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.337, B:E.392, B:D.423, B:E.424, B:D.459 CA.34: 8 residues within 4Å: Chain B: N.425, N.427, A.428, D.457, D.459, N.463, G.464, D.515 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.427, B:D.457, B:D.459, B:N.463, B:D.515 CA.35: 5 residues within 4Å: Chain B: E.442, N.443, N.500, E.502, D.536 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.442, B:E.502, B:D.536 CA.36: 7 residues within 4Å: Chain B: E.442, E.502, D.533, Q.534, D.536, N.537, D.574 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.442, B:E.502, B:D.533, B:Q.534, B:D.536 CA.37: 7 residues within 4Å: Chain B: N.535, N.537, P.539, D.572, D.574, N.578, D.624 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.537, B:D.572, B:D.574, B:N.578, B:D.624

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

CL.19: 3 residues within 4Å: Chain A: N.500, N.537 Ligands: CA.16 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain B: N.500, E.502, N.537 Ligand excluded by PLIP

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

MAN.20: 6 residues within 4Å: Chain A: L.183, M.185, S.191, R.192, S.193 Ligands: MAN.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.193 MAN.21: 5 residues within 4Å: Chain A: E.181, S.193, G.194, T.195 Ligands: MAN.20 No protein-ligand interaction detected (PLIP) MAN.39: 6 residues within 4Å: Chain B: Q.141, L.183, M.185, S.191, R.192, S.193 No protein-ligand interaction detected (PLIP) MAN.40: 5 residues within 4Å: Chain B: E.181, L.183, S.193, G.194, T.195 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.181

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

NA.22: 5 residues within 4Å: Chain A: D.233, L.234, D.235, S.269, G.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.233, A:D.235 NA.41: 4 residues within 4Å: Chain B: D.233, L.234, D.235, S.269 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.233

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 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

protocadherin protein