1VGU Transferase date Nov 03, 2003
title Crystal Structure Of 4-Diphosphocytidyl-2c-Methyl-D-Erythrit Synthase
authors Structural Genomix
compound source
Molecule: 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltran
Chain: A, B
Synonym: 4-Diphosphocytidyl-2c-Methyl-D-Erythritol Synthase Cytidylyltransferase, Mct, Cdp-Me Synthetase;
Ec: 2.7.7.60
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Ispd, B2747
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.268 R_Free 0.333
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.589 66.020 119.475 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand
enzyme Transferase E.C.2.7.7.60 BRENDA
related structures by homologous chain: 1H3M
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural analysis of a set of proteins resulting from a bacterial genomics project., Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ, Proteins. 2005 Sep 1;60(4):787-96. PMID:16021622
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (68 Kb) [Save to disk]
  • Biological Unit Coordinates (1vgu.pdb1.gz) 64 Kb
  • CSU: Contacts of Structural Units for 1VGU
  • Likely Quarternary Molecular Structure file(s) for 1VGU
  • Structure Factors (112 Kb)
  • Retrieve 1VGU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VGU from S2C, [Save to disk]
  • Re-refined 1vgu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VGU 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 1VGU
  • 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 1VGU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vgua_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1vgub_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1vgu 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: [1vgu] [1vgu_A] [1vgu_B]
  • SWISS-PROT database: [Q46893]
  • Domain organization of [ISPD_ECOLI] by SWISSPFAM
  • Other resources with information on 1VGU
  • Community annotation for 1VGU 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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