9EHD | pdb_00009ehd

Crystal structure of N-SH2 domain of SHP2 bound to GAB1 tyrosine phosphorylated peptide (624-633) QVEpYLDLDLD

• PDB DOI: https://doi.org/10.2210/pdb9EHD/pdb

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


• Deposited: 2024-11-22 Released: 2026-01-07 
• Deposition Author(s): Padua, R.A.P., Glaser, A., Ojoawo, A., Kern, D.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.240 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of N-SH2 domain of SHP2 bound to phosphotyrosine

Padua, R.A.P., Glaser, A., Ojoawo, A., Kern, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.51 kDa 
• Atom Count: 945 
• Modeled Residue Count: 110 
• Deposited Residue Count: 119 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 1 of Tyrosine-protein phosphatase non-receptor type 11	A	109	Homo sapiens	Mutation(s): 0  Gene Names: PTPN11, PTP2C, SHPTP2 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q06124 (Homo sapiens) Go to UniProtKB:  Q06124
PHAROS:  Q06124 GTEx:  ENSG00000179295

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphorylated peptide from GRB2-associated-binding protein 1	B	10	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q13480 (Homo sapiens) Explore Q13480  Go to UniProtKB:  Q13480
PHAROS:  Q13480 GTEx:  ENSG00000109458

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.240 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.53	α = 90
b = 61.53	β = 90
c = 73.445	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-07 
Deposition Author(s): Padua, R.A.P., Glaser, A., Ojoawo, A., Kern, D.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2026-01-07
  Type: Initial release