1Y4R Transport Protein date Dec 01, 2004
title T-To-T(High) Quaternary Transitions In Human Hemoglobin: Betaf45a Deoxy Low-Salt (1 Test Set)
authors J.S.Kavanaugh, P.H.Rogers, A.Arnone
compound source
Molecule: Hemoglobin Alpha Chain
Chain: A, C
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood

Molecule: Hemoglobin Beta Chain
Chain: B, D
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hbb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.169 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
97.300 99.800 65.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.22 Å
ligand HEM enzyme
related structures by homologous chain: 1SI4, 1Y0A, 1YEO
Gene
Ontology
ChainFunctionProcessComponent
A, C
  • peroxidase activity


  • D, B
  • peroxidase activity


  • Primary referenceCrystallographic Evidence for a New Ensemble of Ligand-Induced Allosteric Transitions in Hemoglobin: The T-to-T(High) Quaternary Transitions(,)., Kavanaugh JS, Rogers PH, Arnone A, Biochemistry 2005 Apr 26;44(16):6101-21. PMID:15835899
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (1y4r.pdb1.gz) 97 Kb
  • LPC: Ligand-Protein Contacts for 1Y4R
  • CSU: Contacts of Structural Units for 1Y4R
  • Likely Quarternary Molecular Structure file(s) for 1Y4R
  • Structure Factors (236 Kb)
  • Retrieve 1Y4R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y4R from S2C, [Save to disk]
  • Re-refined 1y4r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y4R 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 1Y4R
  • 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 1Y4R, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1y4ra_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1y4rb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1y4rc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1y4rd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1y4r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y4r_C] [1y4r_B] [1y4r_D] [1y4r] [1y4r_A]
  • SWISS-PROT database: [P69905] [P68871]
  • Belongs to the pore-forming globin (globin) family according to TCDB.
  • Belongs to the pore-forming globin (globin) family according to TCDB.
  • Domain organization of [HBA_HUMAN] [HBB_HUMAN] by SWISSPFAM
  • Other resources with information on 1Y4R
  • Community annotation for 1Y4R at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science