1PV8 Lyase date Jun 26, 2003
title Crystal Structure Of A Low Activity F12l Mutant Of Human Porphobilinogen Synthase
authors S.Breinig, J.Kervinen, L.Stith, A.S.Wasson, R.Fairman, A.Wlodawer A.Zdanov, E.K.Jaffe
compound source
Molecule: Delta-Aminolevulinic Acid Dehydratase
Chain: A, B
Synonym: Porphobilinogen Synthase, Aladh
Ec: 4.2.1.24
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Alad
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 63
R_factor 0.199 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
89.571 89.571 153.190 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand PB1, ZN enzyme Lyase E.C.4.2.1.24 BRENDA
related structures by homologous chain: 1E51
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceControl of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase., Breinig S, Kervinen J, Stith L, Wasson AS, Fairman R, Wlodawer A, Zdanov A, Jaffe EK, Nat Struct Biol 2003 Sep;10(9):757-63. Epub 2003 Aug 3. PMID:12897770
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (1pv8.pdb1.gz) 272 Kb
  • LPC: Ligand-Protein Contacts for 1PV8
  • CSU: Contacts of Structural Units for 1PV8
  • Likely Quarternary Molecular Structure file(s) for 1PV8
  • Structure Factors (440 Kb)
  • Retrieve 1PV8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PV8 from S2C, [Save to disk]
  • Re-refined 1pv8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PV8 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 1PV8
  • 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 1PV8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pv8a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1pv8b_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1pv8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1pv8_B] [1pv8] [1pv8_A]
  • SWISS-PROT database: [P13716]
  • Domain organization of [HEM2_HUMAN] by SWISSPFAM
  • Domain found in 1PV8: [ALAD ] by SMART
  • Other resources with information on 1PV8
  • Community annotation for 1PV8 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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