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 Diffraction	resolution	2.80 Å
ligand		enzyme	Transferase E.C.2.7.7.60 BRENDA
related structures	by homologous chain: 1H3M
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structural 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] (67 Kb) [Save to disk] Biological Unit Coordinates (1vgu.pdb1.gz) 63 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

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 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] 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)

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