2HUW | pdb_00002huw

X-ray crystal structure of the Grb2 SH2 domain complexed to a constrained and cyclopropane-derived ligand

• PDB DOI: https://doi.org/10.2210/pdb2HUW/pdb

• Classification: HORMONE/GROWTH FACTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-07-27 Released: 2006-08-15 
• Deposition Author(s): Benfield, A.P., Martin, S.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.227 (Depositor) 
• R-Value Work: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Ligand Preorganization May Be Accompanied by Entropic Penalties in Protein-Ligand Interactions.

Benfield, A.P., Teresk, M.G., Plake, H.R., Delorbe, J.E., Millspaugh, L.E., Martin, S.F.

(2006) Angew Chem Int Ed Engl 45: 6830-6835

• PubMed: 17001728 
• DOI: https://doi.org/10.1002/anie.200600844
• Primary Citation Related Structures: 
  2HUW, 3C7I

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry and The Institute of Cellular and Molecular Biology, University of Texas at Austin, 1 University Station, A5300, 78712-1167, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.52 kDa 
• Atom Count: 1,870 
• Modeled Residue Count: 199 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth factor receptor-bound protein 2	A, B	116	Homo sapiens	Mutation(s): 0  Gene Names: GRB2, ASH
UniProt & NIH Common Fund Data Resources
Find proteins for P62993 (Homo sapiens) Explore P62993  Go to UniProtKB:  P62993
PHAROS:  P62993 GTEx:  ENSG00000177885

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YVN	C [auth A], E [auth B]	N-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-L-valyl-L-aspartamide C21 H30 N5 O9 P LVYNAUCEOQBVSW-RDDKANTKSA-N
PO4	D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.227 (Depositor) 
• R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.824	α = 90
b = 85.49	β = 92.6
c = 41.436	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-15 
Deposition Author(s): Benfield, A.P., Martin, S.F.

Revision History  

• Version 1.0: 2006-08-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations