1BM2 Hormone Growth Factor date Jul 27, 1998
title Grb2-Sh2 Domain In Complex With Cyclo-[N-Alpha-Acetyl-L-Thi Alysyl-O-Phosphotyrosyl-Valyl-Asparagyl-Valyl-Prolyl] (Pkf273-791)
authors J.M.Rondeau, M.Zurini
compound source
Molecule: Protein (Growth Factor Receptor Bound Protein 2)
Chain: A
Fragment: Sh2 Domain
Synonym: Grb2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cellular_location: Cytoplasm
Gene: Grb2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_variant: Plyss
Expression_system_cellular_location: Cytoplasm

Molecule: Protein (Pkf273-791)
Chain: L
Synonym: Cyclo-[N-Alpha-Acetyl-L-Thialysyl-O- Phosphotyrosyl -Valyl-Asparagyl-Valyl- Prolyl];
Engineered: Yes
Other_details: Ace: N-Terminal Acetyl Group Ptr: L- Phosphotyrosine

Synthetic: Yes
symmetry Space Group: P 3 2 1
R_factor 0.197 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.780 83.780 31.990 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand ACE, PTR, SLZ BindingDB enzyme
related structures by homologous chain: 1JYQ, 1TZE
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural and conformational requirements for high-affinity binding to the SH2 domain of Grb2(1)., Ettmayer P, France D, Gounarides J, Jarosinski M, Martin MS, Rondeau JM, Sabio M, Topiol S, Weidmann B, Zurini M, Bair KW, J Med Chem 1999 Mar 25;42(6):971-80. PMID:10090780
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (24 Kb) [Save to disk]
  • Biological Unit Coordinates (1bm2.pdb1.gz) 20 Kb
  • Biological Unit Coordinates (1bm2.pdb2.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 1BM2
  • CSU: Contacts of Structural Units for 1BM2
  • Likely Quarternary Molecular Structure file(s) for 1BM2
  • Structure Factors (84 Kb)
  • Retrieve 1BM2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BM2 from S2C, [Save to disk]
  • Re-refined 1bm2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1BM2 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1BM2
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1BM2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bm2a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1bm2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1bm2] [1bm2_L] [1bm2_A]
  • SWISS-PROT database: [P62993]
  • Domain organization of [GRB2_HUMAN] by SWISSPFAM
  • Domain found in 1BM2: [SH2 ] by SMART
  • Other resources with information on 1BM2
  • Community annotation for 1BM2 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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