SMTL ID : 7za1.1

GPC3-Unc5D octamer structure and role in cell migration

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.10 Å

Oligo State

hetero-4-4-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: 3 residues within 4Å: Chain C: N.149, N.181, T.199 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 10 residues within 4Å: Chain C: S.209, S.210, T.231, T.233, N.234 Chain E: K.73, I.77, N.213, H.217 Ligands: MAN.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.210 NAG-NAG-BMA-MAN.3: 12 residues within 4Å: Chain B: S.209, S.210, T.231, T.233, N.234 Chain F: K.73, I.77, I.209, N.213, H.217 Ligands: MAN.8, MAN.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.210, B:N.234 NAG-NAG-BMA-MAN.4: 12 residues within 4Å: Chain D: W.208, S.209, S.210, T.231, T.233, N.234 Chain G: K.73, I.77, I.209, N.213, H.217 Ligands: MAN.15 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.208, D:N.234 NAG-NAG-BMA-MAN.5: 11 residues within 4Å: Chain A: W.208, S.209, S.210, T.231, T.233, N.234 Chain H: I.77, I.209, N.213, H.217 Ligands: MAN.8 No protein-ligand interaction detected (PLIP)

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

NAG.6: 3 residues within 4Å: Chain A: N.181, S.197, T.199 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain A: V.51, N.70 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain B: N.181, S.197, T.199 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.181, B:N.181 NAG.13: 4 residues within 4Å: Chain B: N.48, E.49, V.51, N.70 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.51 NAG.14: 4 residues within 4Å: Chain D: N.149, N.181, S.197, T.199 No protein-ligand interaction detected (PLIP) NAG.17: 4 residues within 4Å: Chain D: P.23, I.24, A.25, N.70 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.23 NAG.18: 4 residues within 4Å: Chain A: Q.74 Chain E: N.96, A.100, K.103 No protein-ligand interaction detected (PLIP) NAG.19: 3 residues within 4Å: Chain E: E.389, N.390, T.392 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.389, E:N.390, E:T.392 NAG.20: 2 residues within 4Å: Chain D: Q.74 Chain F: N.96 No protein-ligand interaction detected (PLIP) NAG.21: 5 residues within 4Å: Chain B: Q.74 Chain G: N.96, N.99, A.100, K.103 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: G:A.100, G:K.103 Hydrogen bonds: G:K.103, B:Q.74 NAG.22: 6 residues within 4Å: Chain C: Q.74, E.77, D.78 Chain H: N.96, A.100, K.103 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Q.74 Hydrogen bonds: C:Q.74 NAG.23: 3 residues within 4Å: Chain H: E.389, N.390, D.391 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.390

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

MAN.8: 5 residues within 4Å: Chain A: G.207, W.208, R.230 Ligands: NAG-NAG-BMA-MAN.3, NAG-NAG-BMA-MAN.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.208, A:R.230 MAN.9: 4 residues within 4Å: Chain A: S.209, S.210, W.211, R.228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.211, A:R.228, A:R.228 MAN.11: 4 residues within 4Å: Chain B: S.209, S.210, W.211 Ligands: MAN.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.209, B:W.211 MAN.12: 7 residues within 4Å: Chain B: G.207, W.208, R.230 Ligands: NAG-NAG-BMA-MAN.3, NAG-NAG-BMA-MAN.3, NAG-NAG-BMA-MAN.3, MAN.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.208 MAN.15: 8 residues within 4Å: Chain D: G.206, G.207, W.208, R.230, C.244, E.245 Ligands: NAG-NAG-BMA-MAN.2, NAG-NAG-BMA-MAN.4 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.208 MAN.16: 3 residues within 4Å: Chain D: S.209, S.210, W.211 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akkermans, O. et al., GPC3-Unc5 receptor complex structure and role in cell migration. Cell (2022)

Release Date

2022-11-02

Peptides

Netrin receptor UNC5D: ABCD
Glypican-3: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

E
A

F
C

G
D

H
B

Netrin receptor UNC5D

Glypican-3

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