2HUW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Growth factor receptor-bound protein 2
A, B
116Homo sapiensMutation(s): 0 
Gene Names: GRB2 (ASH)
Find proteins for P62993 (Homo sapiens)
Go to Gene View: GRB2
Go to UniProtKB:  P62993
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
YVN
Query on YVN

Download SDF File 
Download CCD File 
A, 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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YVNKa: 1000000 M-1 BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 31.824α = 90.00
b = 85.490β = 92.60
c = 41.436γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
CCP4phasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description