5HNR Lyase date Jan 18, 2016
title The X-Ray Structure Of Octameric Human Native 5-Aminolaevuli Dehydratase.
authors N.L.Mills-Davies, D.Thompson, P.M.Shoolingin-Jordan, P.T.Erskin J.B.Cooper
compound source
Molecule: Delta-Aminolevulinic Acid Dehydratase
Chain: A, B
Synonym: Aladh,Porphobilinogen Synthase
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Blood
symmetry Space Group: I 4 2 2
R_factor 0.165 R_Free 0.238
length a length b length c angle alpha angle beta angle gamma
125.530 125.530 200.910 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.83 Å
ligand DAV, SO4, ZN enzyme Lyase E.C. BRENDA
A, B

Primary referenceStructural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans, Escherichia coli and the hyperthermophile Pyrobaculum calidifontis., Mills-Davies N, Butler D, Norton E, Thompson D, Sarwar M, Guo J, Gill R, Azim N, Coker A, Wood SP, Erskine PT, Coates L, Cooper JB, Rashid N, Akhtar M, Shoolingin-Jordan PM, Acta Crystallogr D Struct Biol. 2017 Jan 1;73(Pt 1):9-21. doi:, 10.1107/S2059798316019525. Epub 2017 Jan 1. PMID:28045381
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk]
  • Biological Unit Coordinates (5hnr.pdb1.gz) 399 Kb
  • LPC: Ligand-Protein Contacts for 5HNR
  • CSU: Contacts of Structural Units for 5HNR
  • Structure Factors (389 Kb)
  • Retrieve 5HNR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5HNR from S2C, [Save to disk]
  • Re-refined 5hnr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5HNR 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 5HNR
  • 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
  • Fold representative 5hnr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5hnr] [5hnr_A] [5hnr_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5HNR: [ALAD ] by SMART
  • Other resources with information on 5HNR
  • Community annotation for 5HNR at PDBWiki (http://pdbwiki.org)

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