5LA9 Oxidoreductase date Jun 14, 2016
title Hif Prolyl Hydroxylase 2 (Phd2-R281cv314c) Cross-Linked To Nodd-L397cd412c And N-Oxalylglycine (Nog) (Complex-2)
authors R.Chowdhury, C.J.Schofield
compound source
Molecule: Egl Nine Homolog 1
Chain: A, B
Fragment: Catalytic Domain Unp Residues 181-426
Synonym: Hypoxia-Inducible Factor Prolyl Hydroxylase 2,Hph- Hydroxylase Domain-Containing Protein 2,Phd2,Sm-20;
Ec: 1.14.11.29
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Egln1, C1orf12, Pnas-118, Pnas-137
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a(+)

Molecule: Hypoxia-Inducible Factor 1-Alpha
Chain: C, D
Fragment: N-Terminal Oxygen Dependent Degradation Domain (N Residues 395-413;
Synonym: Hif1-Alpha,Arnt-Interacting Protein,Basic-Helix-Lo Pas Protein Mop1,Class E Basic Helix-Loop-Helix Protein 78, Member Of Pas Protein 1,Pas Domain-Containing Protein 8;
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Synthetic Peptide
symmetry Space Group: P 21 21 2
R_factor 0.251 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.467 97.329 71.001 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.81 Å
ligand MN, OGA, SO4 enzyme Oxidoreductase E.C.1.14.11.29 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (136 Kb) [Save to disk]
  • Biological Unit Coordinates (5la9.pdb1.gz) 66 Kb
  • Biological Unit Coordinates (5la9.pdb2.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 5LA9
  • CSU: Contacts of Structural Units for 5LA9
  • Structure Factors (264 Kb)
  • Retrieve 5LA9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LA9 from S2C, [Save to disk]
  • Re-refined 5la9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5LA9 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 5LA9
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5la9_D] [5la9] [5la9_C] [5la9_B] [5la9_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5LA9: [P4Hc ] by SMART
  • Other resources with information on 5LA9
  • Community annotation for 5LA9 at PDBWiki (http://pdbwiki.org)

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