9HYT | pdb_00009hyt

Crystal structure of the GFRaL receptor in complex with an inhibitory cyclic peptide

PDB DOI: https://doi.org/10.2210/pdb9HYT/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-01-10 Released: 2025-10-22
Deposition Author(s): Sandmark, J., Ek, M.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.244 (Depositor), 0.247 (DCC)
R-Value Work:
0.194 (Depositor), 0.201 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Design of Bicyclic Peptide Tandems Mimicking the Homodimeric GDF15 Protein to Inhibit GDF15–GFRaL–RET Complex Cell Signaling

Noisier, A.F.M., Sandmark, J., Edfeldt, F., Backmark, A., Broddefalk, J., Wandzik, J., Jurva, U., Ek, M., Johansson, C.A., Barlind, L., Gunnarsson, J., Bigalke, J.M., Xue, Y., Frolov, A.I., Kankkonen, C., Roth, R.G., Fritsch, M., Watcham, S., van Rietschoten, K., Mudd, G.E., Harrison, H., Chen, L., Skynner, M.J., Craik, D.J., Chankeshwara, S.V., Lemurell, M.

(2025) J Med Chem

DOI: https://doi.org/10.1021/acs.jmedchem.5c01378

Macromolecule Content

Total Structure Weight: 89.87 kDa
Atom Count: 5,382
Modeled Residue Count: 641
Deposited Residue Count: 786
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDNF family receptor alpha-like	A, B, C	245	Homo sapiens	Mutation(s): 0 Gene Names: GFRAL, C6orf144, UNQ9356/PRO34128
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UXV0 (Homo sapiens) Explore Q6UXV0 Go to UniProtKB: Q6UXV0
PHAROS: Q6UXV0 GTEx: ENSG00000187871
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6UXV0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inhibitory cyclic peptide	D, E, F	17	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
29N (Subject of Investigation/LOI) Query on 29N Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth F] MOL2 format, chain O [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] mmCIF format, chain O [auth D] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F]	O [auth D], P [auth E], Q [auth F]	1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one C₁₂ H₂₁ N₃ O₃ AEPJNZPJFYDQLM-UHFFFAOYSA-N		Interactions Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F] Interactions & Density Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	G [auth A] H [auth A] J [auth B] K [auth B] L [auth B] G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]