5M7F Transferase date Oct 27, 2016
title Human Porphobilinogen Deaminase In Complex With Dpm Cofactor
authors P.Pluta, O.Millet, P.Roversi, A.L.Rojas, S.Gu
compound source
Molecule: Porphobilinogen Deaminase
Chain: A, B
Synonym: Pbg-D,Hydroxymethylbilane Synthase,Hmbs,Pre-Uropor Synthase;
Ec: 2.5.1.61
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hmbs, Pbgd, Ups
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.220 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.420 80.950 76.220 90.00 95.70 90.00
method X-Ray Diffractionresolution 2.78 Å
ligand DPM, SO4 enzyme Transferase E.C.2.5.1.61 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • hydroxymethylbilane synthase...


  • Primary referenceStructural basis of pyrrole polymerization in human porphobilinogen deaminase., Pluta P, Roversi P, Bernardo-Seisdedos G, Rojas AL, Cooper JB, Gu S, Pickersgill RW, Millet O, Biochim Biophys Acta Gen Subj. 2018 Sep;1862(9):1948-1955. doi:, 10.1016/j.bbagen.2018.06.013. Epub 2018 Jun 15. PMID:29908816
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (412 Kb) [Save to disk]
  • Biological Unit Coordinates (5m7f.pdb1.gz) 205 Kb
  • Biological Unit Coordinates (5m7f.pdb2.gz) 204 Kb
  • LPC: Ligand-Protein Contacts for 5M7F
  • CSU: Contacts of Structural Units for 5M7F
  • Structure Factors (260 Kb)
  • Retrieve 5M7F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5M7F from S2C, [Save to disk]
  • View 5M7F 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 5M7F
  • 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: [5m7f_B] [5m7f_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5M7F
  • Community annotation for 5M7F at PDBWiki (http://pdbwiki.org)

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