2Y34 Oxidoreductase date Dec 18, 2010
title S-Nitrosylated Phd2 (No Exposed) In Complex With Fe(II) And
authors R.Chowdhury, M.A.Mcdonough, C.J.Schofield
compound source
Molecule: Egl Nine Homolog 1
Chain: A
Fragment: Catalytic Domain, Residues 181-426
Synonym: Hypoxia-Inducible Factor Prolyl Hydroxylase 2, Pro Hydroxylase Domain-Containing Protein 2, Sm-20, Hif-Ph2, Hif-Prolyl Hydroxylase 2, Hph-2, Phd2;
Ec: 1.14.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet28a
symmetry Space Group: P 63
R_factor 0.221 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
110.302 110.302 40.378 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.01 Å
ligand FE2, SNC, UN9 BindingDB enzyme Oxidoreductase E.C.1.14.11 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStudies on the Reaction of Nitric Oxide with the Hypoxia-Inducible Factor Prolyl Hydroxylase Domain 2 (EGLN1)., Chowdhury R, Flashman E, Mecinovic J, Kramer HB, Kessler BM, Frapart YM, Boucher JL, Clifton IJ, McDonough MA, Schofield CJ, J Mol Biol. 2011 Jul 8;410(2):268-79. Epub 2011 May 13. PMID:21601578
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (2y34.pdb1.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 2Y34
  • CSU: Contacts of Structural Units for 2Y34
  • Structure Factors (140 Kb)
  • Retrieve 2Y34 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Y34 from S2C, [Save to disk]
  • Re-refined 2y34 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Y34 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 2Y34
  • 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 2Y34, from MSDmotif at EBI
  • Fold representative 2y34 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2y34_A] [2y34]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 2Y34 with the sequences similar proteins can be viewed for 2Y34's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2Y34
  • Community annotation for 2Y34 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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