1VGZ	Transferase	date	Nov 03, 2003
title	Crystal Structure Of 4-Diphosphocytidyl-2c-Methyl-D-Erythrit Synthase
authors	Structural Genomix
compound		source
Molecule: 4-Diphosphocytidyl-2c-Methyl-D-Erythritol Synthas Chain: A, B Ec: 2.7.7.60 Engineered: Yes		Organism_scientific: Neisseria Gonorrhoeae Organism_taxid: 485 Gene: Ygbp Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 31	R_factor 0.274 R_Free 0.318
crystal cell	length a length b length c angle alpha angle beta angle gamma 49.656 49.656 177.809 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	SO4	enzyme	Transferase E.C.2.7.7.60 BRENDA
related structures	by homologous chain: 1VGW
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] (66 Kb) [Save to disk] Biological Unit Coordinates (1vgz.pdb1.gz) 62 Kb LPC: Ligand-Protein Contacts for 1VGZ CSU: Contacts of Structural Units for 1VGZ Likely Quarternary Molecular Structure file(s) for 1VGZ Structure Factors (107 Kb) Retrieve 1VGZ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1VGZ from S2C, [Save to disk] Re-refined 1vgz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1VGZ 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 1VGZ

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 1VGZ, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1vgza_, region A [Jmol] [rasmolscript] [script source]     - Domain d1vgzb_, 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: [1vgz_A] [1vgz_B] [1vgz] SWISS-PROT database: [Q5F829] Domain organization of [ISPD_NEIG1] by SWISSPFAM

Other resources with information on 1VGZ

Community annotation for 1VGZ at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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