2G1M Oxidoreductase date Feb 14, 2006
title Cellular Oxygen Sensing: Crystal Structure Of Hypoxia- Inducible Factor Prolyl Hydroxylase (Phd2)
authors M.A.Mcdonough, C.J.Schofield
compound source
Molecule: Egl Nine Homolog 1
Chain: A
Fragment: Catalytic Domain
Synonym: 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
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Egln1, C1orf12
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28a(+)
symmetry Space Group: P 63
R_factor 0.216 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
110.742 110.742 39.986 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand 4HG, FE2 BindingDB enzyme Oxidoreductase E.C.1.14.11 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)., McDonough MA, Li V, Flashman E, Chowdhury R, Mohr C, Lienard BM, Zondlo J, Oldham NJ, Clifton IJ, Lewis J, McNeill LA, Kurzeja RJ, Hewitson KS, Yang E, Jordan S, Syed RS, Schofield CJ, Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9814-9. Epub 2006 Jun 16. PMID:16782814
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (42 Kb) [Save to disk]
  • Biological Unit Coordinates (2g1m.pdb1.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 2G1M
  • CSU: Contacts of Structural Units for 2G1M
  • Likely Quarternary Molecular Structure file(s) for 2G1M
  • Structure Factors (439 Kb)
  • Retrieve 2G1M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2G1M from S2C, [Save to disk]
  • Re-refined 2g1m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2G1M 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 2G1M
  • 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 2G1M, from MSDmotif at EBI
  • Fold representative 2g1m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2g1m_A] [2g1m]
  • SWISS-PROT database: [Q9GZT9]
  • Domain organization of [EGLN1_HUMAN] by SWISSPFAM
  • Domain found in 2G1M: [P4Hc ] by SMART
  • Alignments of the sequence of 2G1M with the sequences similar proteins can be viewed for 2G1M's classification [EGLN1_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] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2G1M
  • Community annotation for 2G1M 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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