SMTL ID : 6q2j.1

Cryo-EM structure of extracellular dimeric complex of RET/GFRAL/GDF15

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain C: E.261, N.333, S.406 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.261, C:N.333, C:Q.463 NAG.2: 1 residues within 4Å: Chain C: N.308 No protein-ligand interaction detected (PLIP) NAG.3: 2 residues within 4Å: Chain C: T.287, N.349 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.287 NAG.4: 3 residues within 4Å: Chain C: T.250, S.252, N.366 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.250 Hydrogen bonds: C:S.252, C:N.366 NAG.5: 3 residues within 4Å: Chain C: R.390, N.440, D.441 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain C: N.339 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain C: N.56, N.70, R.71 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.70 NAG.12: 3 residues within 4Å: Chain F: E.261, N.333, S.406 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.261, F:N.333, F:Q.463 NAG.13: 1 residues within 4Å: Chain F: N.308 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain F: T.287, N.349 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:T.287 NAG.15: 3 residues within 4Å: Chain F: T.250, S.252, N.366 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:T.250 Hydrogen bonds: F:S.252, F:N.366 NAG.16: 3 residues within 4Å: Chain F: R.390, N.440, D.441 No protein-ligand interaction detected (PLIP) NAG.17: 1 residues within 4Å: Chain F: N.339 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain F: N.56, N.70, R.71 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.70

8 x CA: CALCIUM ION(Non-covalent)

CA.8: 5 residues within 4Å: Chain C: D.238, S.240, D.272, D.274, D.350 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.238, C:S.240, C:D.272, C:D.274, C:D.350 CA.9: 7 residues within 4Å: Chain C: E.150, E.204, D.236, E.237, D.239, A.273, D.274 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.204, C:D.236, C:E.237, C:D.239, C:D.274 CA.10: 5 residues within 4Å: Chain C: E.150, N.151, D.202, E.204, D.239 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.150, C:E.150, C:D.202, C:E.204, C:D.239 CA.11: 6 residues within 4Å: Chain C: T.536, C.537, D.539, H.541, E.546, D.556 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.537, C:D.539, C:H.541, C:E.546, C:E.546 CA.19: 5 residues within 4Å: Chain F: D.238, S.240, D.272, D.274, D.350 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.238, F:S.240, F:D.272, F:D.274, F:D.350 CA.20: 7 residues within 4Å: Chain F: E.150, E.204, D.236, E.237, D.239, A.273, D.274 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.204, F:D.236, F:E.237, F:D.239, F:D.274 CA.21: 5 residues within 4Å: Chain F: E.150, N.151, D.202, E.204, D.239 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.150, F:E.150, F:D.202, F:E.204, F:D.239 CA.22: 6 residues within 4Å: Chain F: T.536, C.537, D.539, H.541, E.546, D.556 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:C.537, F:D.539, F:H.541, F:E.546, F:E.546

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Cryo-EM analyses reveal the common mechanism and diversification in the activation of RET by different ligands. Elife (2019)

Release Date

2019-10-02

Peptides

Growth/differentiation factor 15: AD
GDNF family receptor alpha-like: BE
Proto-oncogene tyrosine-protein kinase receptor Ret: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

B
C

E
D

C
E

F
F

Growth/differentiation factor 15

GDNF family receptor alpha-like

Proto-oncogene tyrosine-protein kinase receptor Ret

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