7R2M

SYNJ2BP complex with a synthetic Vangl2 peptide (9mer).

PDB DOI: https://doi.org/10.2210/pdb7R2M/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-02-04 Released: 2023-05-17
Deposition Author(s): Carrasco, K., Cousido Siah, A., Gogl, G., Betzi, S., McEwen, A., Kostmann, C., Trave, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.239
R-Value Work: 0.215
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

SYNJ2BP PDZ domain in complex with a synthetic Vangl2 peptide.

Carrasco, K., Cousido Siah, A., Gogl, G., Betzi, S., McEwen, A., Kostmann, C., Trave, G.

To be published.

Macromolecule Content

Total Structure Weight: 101.61 kDa
Atom Count: 6,861
Modelled Residue Count: 846
Deposited Residue Count: 892
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptojanin-2-binding protein,Annexin	A [auth D], B [auth A]	422	Homo sapiens	Mutation(s): 0 Gene Names: SYNJ2BP, OMP25, ANXA2
UniProt & NIH Common Fund Data Resources
Find proteins for P57105 (Homo sapiens) Explore P57105 Go to UniProtKB: P57105
PHAROS: P57105 GTEx: ENSG00000213463
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P57105
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vangl2 peptide	C [auth B], D [auth E]	24	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULK5 (Homo sapiens) Explore Q9ULK5 Go to UniProtKB: Q9ULK5
PHAROS: Q9ULK5 GTEx: ENSG00000162738
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ULK5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE4 (Subject of Investigation/LOI) Query on PE4 Download Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D]	K [auth D]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain I [auth D] SDF format, chain J [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D]	I [auth D], J [auth D], P [auth A], Q [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Focus chain J [auth D] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain I [auth D] Focus chain J [auth D] Focus chain P [auth A] Focus chain Q [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain E [auth D] SDF format, chain G [auth D] SDF format, chain H [auth D] SDF format, chain L [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain R [auth A] MOL2 format, chain F [auth D] MOL2 format, chain E [auth D] MOL2 format, chain G [auth D] MOL2 format, chain H [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth A]	E [auth D] F [auth D] G [auth D] H [auth D] L [auth D] E [auth D], F [auth D], G [auth D], H [auth D], L [auth D], M [auth A], N [auth A], O [auth A], R [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Focus chain F [auth D] Focus chain G [auth D] Focus chain H [auth D] Focus chain L [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth A] Interactions & Density Focus chain E [auth D] Focus chain F [auth D] Focus chain G [auth D] Focus chain H [auth D] Focus chain L [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth A]