8SZ2

Stx2A1 bound to P8 stalk peptide

PDB DOI: https://doi.org/10.2210/pdb8SZ2/pdb

Classification: TOXIN, Hydrolase
Organism(s): Escherichia coli O104:H4, Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-05-26 Released: 2024-05-29
Deposition Author(s): rudolph, M.J., Li, X.P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.211
R-Value Work: 0.173
R-Value Observed: 0.175

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Shiga toxin 2 A1 subunit with peptides that bind at the ribosome binding site and inhibit activity

Rudolph, M.J., Li, X.P.

To be published.

Macromolecule Content

Total Structure Weight: 58.9 kDa
Atom Count: 4,131
Modelled Residue Count: 490
Deposited Residue Count: 514
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shiga-like toxin 2 subunit A	A, B	251	Escherichia coli O104:H4	Mutation(s): 0 Gene Names: stxA2, stx2A, L0103 EC: 3.2.2.22
UniProt
Find proteins for P09385 (Escherichia phage 933W) Explore P09385 Go to UniProtKB: P09385
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09385
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P stalk peptide P8	C [auth P], D [auth Q]	6	Escherichia coli	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	E [auth A], F [auth A]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	I [auth A], J [auth A], K [auth A], N [auth B], O [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B]	G [auth A], H [auth A], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B]	L [auth A], P [auth B], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B]