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 Diffraction	resolution	2.00 Å
ligand	MN, OGA BindingDB	enzyme	Oxidoreductase E.C.1.14.11 BRENDA
Primary reference	Structural 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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] SWISS-PROT database: [Q9GZT9] [Q16665] Domain organization of [EGLN1_HUMAN] [HIF1A_HUMAN] by SWISSPFAM Domain found in 3HQR: [P4Hc ] by SMART Alignments of the sequence of 3HQR with the sequences similar proteins can be viewed for 3HQR's classification [EGLN1_HUMAN] [HIF1A_HUMAN] 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 [EGLN1_HUMAN] [HIF1A_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3HQR

Community annotation for 3HQR at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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