SMTL ID : 8egx.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.69 Å

Oligo State

hetero-1-1-mer

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: 2 residues within 4Å: Chain A: N.435, T.437 No protein-ligand interaction detected (PLIP)

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

NAG.2: 5 residues within 4Å: Chain A: S.139, V.141, Q.217, Q.235, N.237 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.141 Hydrogen bonds: A:S.139 NAG.3: 1 residues within 4Å: Chain A: N.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.84 NAG.13: 1 residues within 4Å: Chain B: N.176 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain B: N.215, F.237 No protein-ligand interaction detected (PLIP)

18 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: N.129, N.131, D.161, D.163, N.167, D.224 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.161, A:D.161, A:D.163, A:N.167, A:D.224 CA.5: 6 residues within 4Å: Chain A: N.244, N.246, D.276, D.278, N.282, D.327 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.246, A:D.276, A:D.278, A:N.282, A:D.327 CA.6: 6 residues within 4Å: Chain A: E.261, D.312, F.313, E.314, D.348 Ligands: CA.7 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.261, A:D.312, A:E.314, A:D.348, A:D.348 CA.7: 7 residues within 4Å: Chain A: E.261, E.314, D.345, V.346, D.348, D.386 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.261, A:E.314, A:V.346, A:D.348, A:D.386 CA.8: 6 residues within 4Å: Chain A: N.347, N.349, D.384, D.386, N.391, D.442 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:N.349, A:D.384, A:D.442, A:D.442 CA.9: 7 residues within 4Å: Chain A: E.146, E.211, D.242, I.243, D.245, D.278 Ligands: CA.10 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.146, A:E.211, A:D.242, A:I.243, A:D.245 CA.10: 6 residues within 4Å: Chain A: E.146, D.147, D.209, E.211, D.245 Ligands: CA.9 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.146, A:D.147, A:D.209, A:E.211, A:D.245 CA.11: 6 residues within 4Å: Chain A: E.53, E.99, D.127, D.130, D.163 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.53, A:E.99, A:D.127, A:D.130, A:D.163 CA.12: 6 residues within 4Å: Chain A: E.53, D.97, R.98, E.99, D.130 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.53, A:E.53, A:E.99, A:D.130, A:D.130 CA.15: 6 residues within 4Å: Chain B: E.12, E.69, D.94, I.95, D.97, D.130 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.12, B:E.69, B:D.94, B:I.95, B:D.97 CA.16: 5 residues within 4Å: Chain B: N.96, H.98, D.130, L.134, D.188 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.98, B:D.130, B:D.130, B:D.188 CA.17: 6 residues within 4Å: Chain B: E.113, E.175, D.206, I.207, D.209, D.242 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.175, B:D.206, B:I.207, B:D.209, B:D.242 CA.18: 5 residues within 4Å: Chain B: H.210, D.240, D.242, N.246, D.295 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.210, B:D.240, B:D.242, B:N.246, B:D.295 CA.19: 5 residues within 4Å: Chain B: E.225, E.282, D.313, A.314, D.316 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.225, B:E.282, B:D.313, B:A.314, B:D.316 CA.20: 3 residues within 4Å: Chain B: R.255, S.258, D.261 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.258, B:D.261 CA.21: 4 residues within 4Å: Chain B: N.315, N.317, P.352, D.405 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:N.317, B:D.405 CA.22: 6 residues within 4Å: Chain B: E.12, E.13, D.67, E.69, D.97, H.98 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.12, B:E.13, B:D.67, B:E.69, B:D.97 CA.23: 4 residues within 4Å: Chain B: E.225, D.280, E.282, N.317 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.282

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 Fat 4: A
Protocadherin-16: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Protocadherin Fat 4

Protocadherin-16

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