3HQR Oxidoreductase Transcription date Jun 08, 2009
title Phd2:Mn:Nog:Hif1-Alpha Substrate Complex
authors R.Chowdhury, M.A.Mcdonough, C.J.Schofield
compound source
Molecule: Egl Nine Homolog 1
Chain: A
Fragment: Phd2 Catalytic Domain, Residues 181-426
Synonym: Prolyl Hydroxylase, Hypoxia-Inducible Factor Prolyl Hydroxylase 2, Hif-Prolyl Hydroxylase 2, Hif-Ph2, Hph-2, Prolyl Hydroxylase Domain-Containing Protein 2, Phd2, Sm-20;
Ec: 1.14.11.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Phd2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a(+)

Molecule: Hypoxia-Inducible Factor 1 Alpha
Chain: S
Fragment: C-Terminal Degradation Domain, Residues 558-574
Synonym: Hif-1 Alpha, Hif1 Alpha, Arnt-Interacting Protein, Member Of Pas Protein 1, Basic-Helix-Loop-Helix-Pas Protein Mop1;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Peptide Synthesis
symmetry Space Group: P 21 21 21
R_factor 0.234 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.379 68.798 72.221 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand MN, OGA BindingDB enzyme Oxidoreductase E.C.1.14.11 BRENDA
Primary referenceStructural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases., Chowdhury R, McDonough MA, Mecinovic J, Loenarz C, Flashman E, Hewitson KS, Domene C, Schofield CJ, Structure. 2009 Jul 15;17(7):981-9. PMID:19604478
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (3hqr.pdb1.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 3HQR
  • CSU: Contacts of Structural Units for 3HQR
  • Likely Quarternary Molecular Structure file(s) for 3HQR
  • Structure Factors (101 Kb)
  • Retrieve 3HQR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HQR from S2C, [Save to disk]
  • Re-refined 3hqr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HQR 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 3HQR
  • 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 3HQR, from MSDmotif at EBI
  • Fold representative 3hqr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hqr_A] [3hqr_S] [3hqr]
  • SWISS-PROT database: [Q9GZT9] [Q16665]
  • Domain organization of [EGLN1_HUMAN] [HIF1A_HUMAN] by SWISSPFAM
  • Domain found in 3HQR: [P4Hc ] by SMART
  • Other resources with information on 3HQR
  • Community annotation for 3HQR 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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