SMTL ID : 8egw.1

Complex of Fat4(EC1-4) bound to Dchs1(EC1-3)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

2 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: N.217, Q.218, F.239 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: N.84, T.87 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- FUC- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC-FUC.3: 5 residues within 4Å: Chain B: N.435, T.437, V.458, S.460, V.462 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.458

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.4: 6 residues within 4Å: Chain B: S.139, I.140, V.141, Q.217, Q.235, N.237 No protein-ligand interaction detected (PLIP)

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

NAG.5: 1 residues within 4Å: Chain A: N.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.178

19 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: E.115, H.116, D.175, E.177, D.211 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.115, A:H.116, A:D.175, A:E.177, H2O.2 CA.7: 6 residues within 4Å: Chain A: N.210, H.212, D.242, D.244, N.248, D.297 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.212, A:D.242, A:D.244, A:N.248, A:D.297 CA.8: 6 residues within 4Å: Chain A: E.115, E.177, D.208, I.209, D.211, D.244 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:E.115, A:E.177, A:D.208, A:I.209, A:D.211, A:D.244 CA.9: 6 residues within 4Å: Chain A: N.98, H.100, D.130, D.132, L.136, D.190 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.100, A:D.130, A:D.132, A:L.136, A:D.190 CA.10: 7 residues within 4Å: Chain A: E.14, E.71, D.96, I.97, D.99, H.100, D.132 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.14, A:E.71, A:E.71, A:D.96, A:D.132 CA.11: 5 residues within 4Å: Chain A: E.14, E.15, D.69, E.71, D.99 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.14, A:E.15, A:D.69, A:E.71, A:D.99 CA.12: 2 residues within 4Å: Chain A: E.227, D.315 No protein-ligand interaction detected (PLIP) CA.13: 1 residues within 4Å: Chain A: R.258 No protein-ligand interaction detected (PLIP) CA.19: 6 residues within 4Å: Chain B: N.129, N.131, D.161, D.163, N.167, D.224 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.131, B:D.161, B:D.163, B:N.167, B:D.224 CA.20: 8 residues within 4Å: Chain B: E.53, E.99, D.127, L.128, D.130, N.131, D.163 Ligands: CA.21 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.53, B:E.99, B:L.128, B:D.130, B:D.163 CA.21: 6 residues within 4Å: Chain B: E.53, E.54, D.97, E.99, D.130 Ligands: CA.20 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.53, B:D.97, B:E.99, B:D.130, H2O.9 CA.22: 4 residues within 4Å: Chain B: E.146, D.209, E.211, D.245 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.146, B:D.209, B:E.211, B:D.245, H2O.8 CA.23: 7 residues within 4Å: Chain B: E.146, E.211, D.242, I.243, D.245, N.246, D.278 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.146, B:E.211, B:D.242, B:I.243, B:D.278 CA.24: 8 residues within 4Å: Chain B: E.261, E.314, D.345, V.346, D.348, N.349, D.386 Ligands: CA.25 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.261, B:E.314, B:V.346, B:D.348, B:D.386 CA.25: 5 residues within 4Å: Chain B: E.261, D.312, E.314, D.348 Ligands: CA.24 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.261, B:D.312, B:E.314, H2O.8, H2O.9 CA.26: 6 residues within 4Å: Chain B: N.347, N.349, D.384, D.386, N.391, D.442 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.349, B:D.384, B:D.384, B:D.386, B:D.442 CA.27: 6 residues within 4Å: Chain B: N.244, N.246, D.276, D.278, N.282, D.327 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.246, B:D.276, B:D.278, B:N.282, B:D.327 CA.28: 2 residues within 4Å: Chain B: S.412, K.413 No protein-ligand interaction detected (PLIP) CA.29: 1 residues within 4Å: Chain B: D.278 No protein-ligand interaction detected (PLIP)

3 x CAC: CACODYLATE ION(Non-covalent)

CAC.14: 5 residues within 4Å: Chain A: S.219, S.306, A.307, F.308 Chain B: Q.153 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:S.306 Hydrogen bonds: B:Q.153 CAC.16: 2 residues within 4Å: Chain A: Q.276, E.278 No protein-ligand interaction detected (PLIP) CAC.18: 7 residues within 4Å: Chain A: G.134, R.135, T.138, Q.139, D.161, G.162, P.164 No protein-ligand interaction detected (PLIP)

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

EDO.15: 3 residues within 4Å: Chain A: F.239, A.240 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.240 EDO.17: 6 residues within 4Å: Chain A: A.215, F.216, N.217, F.239, S.241 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.216, A:S.241 EDO.30: 2 residues within 4Å: Chain B: R.172, I.189 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.189 EDO.31: 5 residues within 4Å: Chain B: V.169, D.170, H.171, R.172, K.225 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.171, B:K.225 EDO.32: 6 residues within 4Å: Chain A: E.303 Chain B: T.143, F.144, K.145, S.148, Q.153 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.145, B:S.148, B:Q.153, A:E.303 EDO.33: 6 residues within 4Å: Chain B: N.349, D.350, V.352, T.383, D.384, A.385 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.383, B:A.385 EDO.34: 6 residues within 4Å: Chain B: N.131, A.132, V.134, T.160, D.161, S.162 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.160, B:D.161, B:S.162, B:S.162 EDO.35: 3 residues within 4Å: Chain B: E.44, P.45, R.67 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.44, B:R.67, B:R.67 Water bridges: B:E.44, B:E.44 EDO.36: 3 residues within 4Å: Chain B: P.138, Y.233, Q.235 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.233 EDO.37: 7 residues within 4Å: Chain A: Q.44 Chain B: V.382, T.383, D.384, N.391, I.394, N.416 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.384, B:N.391, A:Q.44, A:Q.44 EDO.38: 4 residues within 4Å: Chain B: R.286, D.327, R.328, S.332 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.327, B:R.328, B:S.332 EDO.39: 8 residues within 4Å: Chain A: Y.39, F.40, I.41, E.57 Chain B: R.356, Y.357, F.358, A.360 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.356, A:I.41, A:I.41 Water bridges: B:F.358, A:E.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medina, E. et al., Structure of the planar cell polarity cadherins Fat4 and Dachsous1. Nat Commun (2023)

Release Date

2023-02-22

Peptides

Protocadherin-16: A
Protocadherin Fat 4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protocadherin-16

Protocadherin Fat 4

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