1FYR Hormone Growth Factor date Oct 03, 2000
title Dimer Formation Through Domain Swapping In The Crystal Structure Of The Grb2-Sh2 Ac-Pyvnv Complex
authors N.Schiering, E.Casale, P.Caccia, P.Giordano, C.Battistini
compound source
Molecule: Growth Factor Receptor-Bound Protein 2
Chain: A, B, C, D
Fragment: Sh2 Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pgex-2t

Molecule: Hepatocyte Growth Factor Receptor Peptide
Chain: I, J, K, L
Fragment: Residues 1356-1359 (Residues 0-3 In Coordinates)
Engineered: Yes
Other_details: The Sequence Yvnv Is Also Found In Other Proteins

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized. The Sequence Occurs Naturally In Humans.
symmetry Space Group: P 43 21 2
R_factor 0.217 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.610 77.610 183.470 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand ACE, PTR BindingDB enzyme
related structures by homologous chain: 1JYU, 1TZE
Primary referenceDimer formation through domain swapping in the crystal structure of the Grb2-SH2-Ac-pYVNV complex., Schiering N, Casale E, Caccia P, Giordano P, Battistini C, Biochemistry 2000 Nov 7;39(44):13376-82. PMID:11063574
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (1fyr.pdb1.gz) 37 Kb
  • Biological Unit Coordinates (1fyr.pdb2.gz) 37 Kb
  • Biological Unit Coordinates (1fyr.pdb3.gz) 72 Kb
  • Biological Unit Coordinates (1fyr.pdb4.gz) 72 Kb
  • Biological Unit Coordinates (1fyr.pdb5.gz) 55 Kb
  • Biological Unit Coordinates (1fyr.pdb6.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 1FYR
  • CSU: Contacts of Structural Units for 1FYR
  • Likely Quarternary Molecular Structure file(s) for 1FYR
  • Retrieve 1FYR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1FYR from S2C, [Save to disk]
  • View 1FYR 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 1FYR
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1FYR, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1fyra_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1fyrb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1fyrc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1fyrd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1fyr 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: [1fyr] [1fyr_A] [1fyr_B] [1fyr_K] [1fyr_I] [1fyr_J] [1fyr_L] [1fyr_C] [1fyr_D]
  • SWISS-PROT database: [P62993] [P08581]
  • Domain organization of [GRB2_HUMAN] [MET_HUMAN] by SWISSPFAM
  • Domain found in 1FYR: [SH2 ] by SMART
  • Other resources with information on 1FYR
  • Community annotation for 1FYR 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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