3D4J Lyase date May 14, 2008
title Crystal Structure Of Human Mevalonate Diphosphate Decarboxylase
authors N.E.Voynova, Z.Fu, K.Battaile, T.J.Herdendorf, J.J.P.Kim, H.M.Miziorko
compound source
Molecule: Diphosphomevalonate Decarboxylase
Chain: A, B
Synonym: Mevalonate Pyrophosphate Decarboxylase, Mevalonate (Diphospho)Decarboxylase;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Man
Organism_taxid: 9606
Gene: Mvd, Mpd
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-3d
symmetry Space Group: P 1 21 1
R_factor 0.218 R_Free 0.274
length a length b length c angle alpha angle beta angle gamma
86.960 53.190 97.790 90.00 107.25 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand SO4 enzyme Lyase E.C. BRENDA
A, B

Primary referenceHuman mevalonate diphosphate decarboxylase: characterization, investigation of the mevalonate diphosphate binding site, and crystal structure., Voynova NE, Fu Z, Battaile KP, Herdendorf TJ, Kim JJ, Miziorko HM, Arch Biochem Biophys. 2008 Dec 1;480(1):58-67. Epub 2008 Sep 18. PMID:18823933
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (3d4j.pdb1.gz) 118 Kb
  • LPC: Ligand-Protein Contacts for 3D4J
  • CSU: Contacts of Structural Units for 3D4J
  • Likely Quarternary Molecular Structure file(s) for 3D4J
  • Structure Factors (265 Kb)
  • Retrieve 3D4J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D4J from S2C, [Save to disk]
  • Re-refined 3d4j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D4J 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 3D4J
  • 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 3D4J, from MSDmotif at EBI
  • Fold representative 3d4j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d4j_A] [3d4j] [3d4j_B]
  • SWISS-PROT database: [P53602]
  • Domain organization of [ERG19_HUMAN] by SWISSPFAM
  • Other resources with information on 3D4J
  • Community annotation for 3D4J 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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