SMTL ID : 7za3.1

GPC3-Unc5D octamer structure and role in cell migration

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.00 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 H: N.149, N.181, T.199 No protein-ligand interaction detected (PLIP)

14 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.2: 7 residues within 4Å: Chain A: I.209, N.213, H.217 Chain G: S.209, S.210, T.233, N.234 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: G:N.234 Hydrogen bonds: G:S.210, G:S.210, G:S.210, A:N.213 NAG.3: 5 residues within 4Å: Chain B: R.92, H.93, N.96, Y.97, A.100 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.93, B:N.96 Hydrogen bonds: B:H.93, B:N.96, B:Y.97 NAG.4: 9 residues within 4Å: Chain B: I.77, I.209, N.213, H.217 Chain H: S.209, S.210, T.231, T.233, N.234 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:N.234, H:N.234, B:N.213 NAG.5: 2 residues within 4Å: Chain C: N.96 Chain G: D.78 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.96 NAG.6: 8 residues within 4Å: Chain C: Q.66, K.73, N.213, D.216, H.217 Chain E: S.209, S.210, N.234 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:K.73 Hydrogen bonds: C:K.73, E:N.234 NAG.7: 5 residues within 4Å: Chain D: N.96, N.99, A.100, K.103, F.114 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.103 Hydrogen bonds: D:N.96 NAG.8: 10 residues within 4Å: Chain D: K.73, I.77, I.209, N.213, H.217 Chain F: S.209, S.210, T.231, T.233, N.234 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.210, F:S.210, F:N.234 NAG.10: 8 residues within 4Å: Chain E: P.23, I.24, A.25, L.26, V.51, F.68, N.70, V.71 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:A.25 Hydrogen bonds: E:A.25, E:N.70 NAG.11: 3 residues within 4Å: Chain E: N.149, N.181, T.199 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.181 NAG.12: 4 residues within 4Å: Chain F: P.23, I.24, A.25, N.70 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.70 NAG.13: 3 residues within 4Å: Chain F: N.149, N.181, T.199 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.181 NAG.15: 5 residues within 4Å: Chain G: P.23, A.25, F.68, I.69, N.70 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:A.25, G:F.68 NAG.16: 4 residues within 4Å: Chain G: N.149, G.180, N.181, T.199 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:N.181 Hydrogen bonds: G:N.181, G:T.199 NAG.18: 5 residues within 4Å: Chain H: I.24, A.25, V.51, F.68, N.70 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:A.25

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

MAN.9: 4 residues within 4Å: Chain E: G.206, G.207, W.208, R.230 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:W.208, E:R.230 MAN.14: 4 residues within 4Å: Chain F: S.209, S.210, W.211, R.230 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:W.211 MAN.17: 4 residues within 4Å: Chain G: W.208, R.230, C.244, E.245 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.230

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

Glypican-3: ABCD
Netrin receptor UNC5D: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Glypican-3

Netrin receptor UNC5D

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