› 5x94

X-ray diffraction
2.6Å resolution

Crystal structure of SHP2_SH2-CagA EPIYA_D peptide complex

Released:
DOI: 10.2210/pdb5x94/pdb
PDB entry 5x94 coloured by chain, front view.
PDB entry 5x94 coloured by chain, side view.
PDB entry 5x94 coloured by chain, top view.
Source organisms:
Primary publication:
Differential Mechanisms for SHP2 Binding and Activation Are Exploited by Geographically Distinct Helicobacter pylori CagA Oncoproteins.
Hayashi T, Senda M, Suzuki N, Nishikawa H, Ben C, Tang C, Nagase L, Inoue K, Senda T, Hatakeyama M
Cell Rep 20 2876-2890 (2017)
PMID: 28930683

Function and Biology Details

Reaction catalysed: 
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157377 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Tyrosine-protein phosphatase non-receptor type 11 Chains: A, B
Molecule details ›
Chains: A, B
Length: 220 amino acids
Theoretical weight: 25.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q06124 (Residues: 1-220; Coverage: 37%)
Gene names: PTP2C, PTPN11, SHPTP2
Sequence domains: SH2 domain
Structure domains: SH2 domain
Cytotoxicity-associated immunodominant antigen Chains: L, M, N, O
Molecule details ›
Chains: L, M, N, O
Length: 13 amino acids
Theoretical weight: 1.52 KDa
Source organism: Helicobacter pylori F32
Expression system: Not provided
UniProt:
  • Canonical: P55980 (Residues: 966-976; Coverage: 1%)
Gene names: HP_0547, cag26, cagA, cai

Ligands and Environments

No bound ligands
2 modified residues:
Ligand MSE 8 x MSE
Ligand PTR 4 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P21
Unit cell:
a: 28.184Å b: 121.968Å c: 72.171Å
α: 90° β: 101.26° γ: 90°
R-values:
R R work R free
0.163 0.157 0.246
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

13 review citations

Global burden of gastric cancer: epidemiological trends, risk factors, screening and prevention.
Thrift et al. (2023)
12 more

7 mentions without citation

Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase.
Anselmi et al. (2020)
6 more