8AEL | pdb_00008ael

SYNJ2BP complex with a synthetic Vangl2 peptide (3mer).

PDB DOI: https://doi.org/10.2210/pdb8AEL/pdb

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

Deposited: 2022-07-13 Released: 2023-08-16
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: 2.20 Å
R-Value Free:
0.264 (Depositor), 0.265 (DCC)
R-Value Work:
0.221 (Depositor)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 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: 48.24 kDa
Atom Count: 3,581
Modeled Residue Count: 423
Deposited Residue Count: 423
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptojanin-2-binding protein,Annexin A2	A	417	Homo sapiens	Mutation(s): 0 Gene Names: SYNJ2BP, OMP25, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D
UniProt & NIH Common Fund Data Resources
Find proteins for P07355 (Homo sapiens) Explore P07355 Go to UniProtKB: P07355
PHAROS: P07355 GTEx: ENSG00000182718
Find proteins for P57105 (Homo sapiens) Explore P57105 Go to UniProtKB: P57105
PHAROS: P57105 GTEx: ENSG00000213463
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P07355 P57105
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-GLY-GLY-THR-SER-VAL	B	6	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]