2RG8 Apoptosis, Translation date Oct 03, 2007
title Crystal Structure Of Programmed For Cell Death 4 Middle Ma3
authors R.Garces, C.Suzuki, G.Wagner
compound source
Molecule: Programmed Cell Death Protein 4
Chain: A, B
Fragment: Ma3 Domain
Synonym: Nuclear Antigen H731-Like, Neoplastic Transformati Inhibitor Protein, Protein 19715a;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdcd4, H731
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 21 21 21
R_factor 0.202 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
37.680 70.060 110.880 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CL, MSE, NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referencePDCD4 inhibits translation initiation by binding to eIF4A using both its MA3 domains., Suzuki C, Garces RG, Edmonds KA, Hiller S, Hyberts SG, Marintchev A, Wagner G, Proc Natl Acad Sci U S A. 2008 Feb 22;. PMID:18296639
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (2rg8.pdb1.gz) 28 Kb
  • Biological Unit Coordinates (2rg8.pdb2.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 2RG8
  • CSU: Contacts of Structural Units for 2RG8
  • Likely Quarternary Molecular Structure file(s) for 2RG8
  • Structure Factors (254 Kb)
  • Retrieve 2RG8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2RG8 from S2C, [Save to disk]
  • Re-refined 2rg8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2RG8 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 2RG8
  • 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 2RG8, from MSDmotif at EBI
  • Fold representative 2rg8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2rg8_A] [2rg8] [2rg8_B]
  • SWISS-PROT database: [Q53EL6]
  • Domain organization of [PDCD4_HUMAN] by SWISSPFAM
  • Domain found in 2RG8: [MA3 ] by SMART
  • Other resources with information on 2RG8
  • Community annotation for 2RG8 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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