3IMJ

Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pTyr-Ile-Asn-NH2 Tripeptide Mimic

Structural Biology Knowledgebase: 3IMJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.200

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3IMJ

Classification: SIGNALING PROTEIN / PEPTIDE

Total Structure Weight: 28600.36

Macromolecule Entities
Molecule Chains Length Organism Details
Growth factor receptor-bound protein 2 A, B 117 Homo sapiens Fragment: SH2 domain
Gene Name(s): GRB2 Gene View ASH

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AYI
Query on AYI

A, B (1R,2S,3R,1S',1S")Phosphoric acid mono(4- {2-[1-(1,2-dicarbamoylethylcarbamoyl)-3-carbamoylpropylcarbamoyl]- 3-methylcarbamoylcyclopropyl}phenyl) ester
C22 H32 N5 O9 P
TXAWBRUKEBJWOA-LWVFFRLXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
AYI N/A in BindingDB
Ka: 2.1e+06 M-1  BindingMOAD
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000632 (AY0,ASN,NH2,ILE) A, B CYCLOPROPYL-CONSTRAINED AC-PTYR-ILE-ASN-NH2 TRIPEPTIDE MIMIC Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.200
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 31.59 α = 90.00
b = 85.51 β = 98.47
c = 41.64 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-08-10
  • Released Date: 2009-11-17
  • Deposition author(s): Clements, J.H.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords