2L4K | pdb_00002l4k

Water refined solution structure of the human Grb7-SH2 domain in complex with the 10 amino acid peptide pY1139

• PDB DOI: https://doi.org/10.2210/pdb2L4K/pdb

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


• Deposited: 2010-10-07 Released: 2010-11-17 
• Deposition Author(s): Pias, S.C., Ivancic, M., Brescia, P.J., Johnson, D.L., Smith, D.E., Daly, R.J., Lyons, B.A.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy and the fewest restraint violations 

Literature

Water-Refined Solution Structure of the Human Grb7-SH2 Domain in Complex with the erbB2 Receptor Peptide pY1139.

Pias, S.C., Johnson, D.L., Smith, D.E., Lyons, B.A.

(2012) Protein Pept Lett 19: 832-838

• PubMed: 22702899 
• DOI: https://doi.org/10.2174/092986612801619543
• Primary Citation Related Structures: 
  2L4K


• PubMed Abstract: 
  

  We report a refinement in implicit water of the previously published solution structure of the Grb7-SH2 domain bound to the erbB2 receptor peptide pY1139. Structure quality measures indicate substantial improvement, with residues in the most favored regions of the Ramachandran plot increasing by 14 % and with WHAT IF statistics (Vriend, G. J. Mol. Graph., 1990, 8(1), 52-56) falling closer to expected values for well-refined structures.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003-8001, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.96 kDa 
• Atom Count: 1,050 
• Modeled Residue Count: 130 
• Deposited Residue Count: 130 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth factor receptor-bound protein 7	A	120	Homo sapiens	Mutation(s): 0  Gene Names: GRB7
UniProt & NIH Common Fund Data Resources
Find proteins for Q14451 (Homo sapiens) Explore Q14451  Go to UniProtKB:  Q14451
PHAROS:  Q14451 GTEx:  ENSG00000141738

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	B	10	Homo sapiens	Mutation(s): 0  EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens) Explore P04626  Go to UniProtKB:  P04626
PHAROS:  P04626 GTEx:  ENSG00000141736

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: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy and the fewest restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Pias, S.C., Ivancic, M., Brescia, P.J., Johnson, D.L., Smith, D.E., Daly, R.J., Lyons, B.A.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-07-25
  Changes: Database references
• Version 1.3: 2012-10-03
  Changes: Database references
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary