9EQ6 | pdb_00009eq6

Cachd1 and FZD5 complex

PDB DOI: https://doi.org/10.2210/pdb9EQ6/pdb

Classification: SIGNALING PROTEIN
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-03-20 Released: 2025-04-02
Deposition Author(s): Zhao, Y., Ren, J., Jones, E.Y.
Funding Organization(s): Cancer Research UK, Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.286 (Depositor), 0.288 (DCC)
R-Value Work:
0.258 (Depositor), 0.260 (DCC)
R-Value Observed:
0.260 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Cachd1 is a Frizzled- and LRP6-interacting protein required for neurons to acquire left-right asymmetric character

Zhao, Y., Ren, J., Jones, E.Y.

To be published.

Macromolecule Content

Total Structure Weight: 140.63 kDa
Atom Count: 9,193
Modelled Residue Count: 1,158
Deposited Residue Count: 1,242
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Frizzled-5	A [auth B]	140	Mus musculus	Mutation(s): 0 Gene Names: Fzd5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9EQD0 (Mus musculus) Explore Q9EQD0 Go to UniProtKB: Q9EQD0
IMPC: MGI:108571
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9EQD0
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth B]	Go to GlyGen: Q9EQD0-1
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VWFA and cache domain-containing protein 1	B [auth A]	1,102	Mus musculus	Mutation(s): 0 Gene Names: Cachd1, Kiaa1573, Vwcd1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PDJ1 (Mus musculus) Explore Q6PDJ1 Go to UniProtKB: Q6PDJ1
IMPC: MGI:2444177
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6PDJ1
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain B [auth A]	Go to GlyGen: Q6PDJ1-1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	C [auth B] D [auth A] E [auth A] F [auth A] G [auth A] C [auth B], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]