3C7I | pdb_00003c7i

X-RAY crystal structure of the complex between the grb2-sh2 domain and a flexible ligand, FPTVN.

• PDB DOI: https://doi.org/10.2210/pdb3C7I/pdb
• Entry: 3C7I supersedes: 2HUY

• Classification: SPLICING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-07 Released: 2008-08-12 
• Deposition Author(s): Benfield, A.P., Martin, S.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.234 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (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 118: 6984-6989

• 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 14.26 kDa 
• Atom Count: 992 
• Modeled Residue Count: 101 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth factor receptor-bound protein 2	A	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
TVN	B [auth A]	N-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-valyl-L-aspartamide C21 H32 N5 O9 P CCEFGGFBPGVHRR-XUWXXGDYSA-N
FMT	C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.234 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.053	α = 90
b = 42.053	β = 90
c = 109.426	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Benfield, A.P., Martin, S.F.
• This entry supersedes: 2HUY

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations