SMTL ID : 6q2s.1

Cryo-EM structure of RET/GFRa3/ARTN extracellular complex. The 3D refinement was applied with C2 symmetry.

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 B: S.275, N.278, S.280 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.275, B:S.280, B:S.280 NAG.2: 1 residues within 4Å: Chain C: N.308 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.308, C:N.308 NAG.3: 4 residues within 4Å: Chain C: R.284, R.285, T.287, N.349 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.287 Hydrogen bonds: C:N.349 NAG.4: 1 residues within 4Å: Chain C: N.366 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain C: N.440, D.441 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain C: N.70 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.70 NAG.7: 1 residues within 4Å: Chain C: N.333 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain E: S.275, N.278, S.280 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.275, E:S.280, E:S.280 NAG.13: 1 residues within 4Å: Chain F: N.308 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.308, F:N.308 NAG.14: 4 residues within 4Å: Chain F: R.284, R.285, T.287, N.349 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:T.287 Hydrogen bonds: F:N.349 NAG.15: 1 residues within 4Å: Chain F: N.366 No protein-ligand interaction detected (PLIP) NAG.16: 2 residues within 4Å: Chain F: N.440, D.441 No protein-ligand interaction detected (PLIP) NAG.17: 1 residues within 4Å: Chain F: N.70 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.70 NAG.18: 1 residues within 4Å: Chain F: N.333 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain C: D.238, S.240, D.272, D.274, Y.286, 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: 8 residues within 4Å: Chain C: E.150, E.204, D.236, E.237, D.239, A.273, D.274 Ligands: CA.10 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: 6 residues within 4Å: Chain C: E.150, N.151, D.202, E.204, D.239 Ligands: CA.9 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: 8 residues within 4Å: Chain C: T.536, C.537, P.538, D.539, H.541, E.546, C.553, D.556 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:T.536, C:C.537, C:D.539, C:H.541, C:E.546 CA.19: 6 residues within 4Å: Chain F: D.238, S.240, D.272, D.274, Y.286, 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: 8 residues within 4Å: Chain F: E.150, E.204, D.236, E.237, D.239, A.273, D.274 Ligands: CA.21 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: 6 residues within 4Å: Chain F: E.150, N.151, D.202, E.204, D.239 Ligands: CA.20 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: 8 residues within 4Å: Chain F: T.536, C.537, P.538, D.539, H.541, E.546, C.553, D.556 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:T.536, F:C.537, F:D.539, F:H.541, 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

Ubiquitin-like protein SMT3,Artemin: AD
GDNF family receptor alpha-3: 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

Ubiquitin-like protein SMT3,Artemin

GDNF family receptor alpha-3

Proto-oncogene tyrosine-protein kinase receptor Ret

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