5L9V	Oxidoreductase	date	Jun 11, 2016
title	Hif Prolyl Hydroxylase 2 (Phd2-R281cp317c) Cross-Linked To Nodd-L397cd412c And N-Oxalylglycine (Nog) (Complex-1)
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 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: 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 1 21 1	R_factor 0.169 R_Free 0.190
crystal cell	length a length b length c angle alpha angle beta angle gamma 43.807 73.088 70.407 90.00 91.17 90.00
method	X-Ray Diffraction	resolution	1.83 Å
ligand	MN, OGA	enzyme	Oxidoreductase E.C.1.14.11.29 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases., Chowdhury R, Leung IK, Tian YM, Abboud MI, Ge W, Domene C, Cantrelle FX, Landrieu I, Hardy AP, Pugh CW, Ratcliffe PJ, Claridge TD, Schofield CJ, Nat Commun. 2016 Aug 26;7:12673. doi: 10.1038/ncomms12673. PMID:27561929

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk] Biological Unit Coordinates (5l9v.pdb1.gz) 72 Kb Biological Unit Coordinates (5l9v.pdb2.gz) 71 Kb LPC: Ligand-Protein Contacts for 5L9V CSU: Contacts of Structural Units for 5L9V Structure Factors (658 Kb) Retrieve 5L9V in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5L9V from S2C, [Save to disk] Re-refined 5l9v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5L9V 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 5L9V

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: [5l9v_C] [5l9v_B] [5l9v_A] [5l9v] [5l9v_D] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 5L9V: [P4Hc ] by SMART

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