8S7C

Ternary Complex of Cachd1, FZD5 and LRP6

PDB DOI: https://doi.org/10.2210/pdb8S7C/pdb

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

Deposited: 2024-02-29 Released: 2024-04-24
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: 4.70 Å
R-Value Free: 0.261
R-Value Work: 0.206
R-Value Observed: 0.209

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.

(2024) Science

DOI: https://doi.org/10.1126/science.ade6970

Macromolecule Content

Total Structure Weight: 637.94 kDa
Atom Count: 41,714
Modelled Residue Count: 5,229
Deposited Residue Count: 5,610
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VWFA and cache domain-containing protein 1	A, D, G	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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Frizzled-5	B, E, H	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
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Low-density lipoprotein receptor-related protein 6	C, F, I	628	Homo sapiens	Mutation(s): 0 Gene Names: LRP6
UniProt & NIH Common Fund Data Resources
Find proteins for O75581 (Homo sapiens) Explore O75581 Go to UniProtKB: O75581
PHAROS: O75581 GTEx: ENSG00000070018
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75581
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, K	2		N-Glycosylation	Interactions Focus chain J Focus chain K Interactions & Density Focus chain J Focus chain K

Small Molecules

Ligands 1 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 AA [auth F] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain EA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain KA [auth G] SDF format, chain L [auth A] SDF format, chain LA [auth H] SDF format, chain M [auth A] SDF format, chain MA [auth I] SDF format, chain N [auth A] SDF format, chain NA [auth I] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain DA [auth F] SDF format, chain IA [auth G] SDF format, chain JA [auth G] SDF format, chain OA [auth I] SDF format, chain S [auth C] SDF format, chain Z [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain DA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain JA [auth G] MOL2 format, chain OA [auth I] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth E]	AA [auth F] BA [auth F] CA [auth F] DA [auth F] EA [auth F] AA [auth F], BA [auth F], CA [auth F], DA [auth F], EA [auth F], FA [auth G], GA [auth G], HA [auth G], IA [auth G], JA [auth G], KA [auth G], L [auth A], LA [auth H], M [auth A], MA [auth I], N [auth A], NA [auth I], O [auth A], OA [auth I], P [auth A], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth D], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain L [auth A] Focus chain LA [auth H] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain NA [auth I] Focus chain O [auth A] Focus chain OA [auth I] Focus chain P [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain L [auth A] Focus chain LA [auth H] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain NA [auth I] Focus chain O [auth A] Focus chain OA [auth I] Focus chain P [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth E]