1VGW	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, C, D, E, F Ec: 2.7.7.- Engineered: Yes		Organism_scientific: Neisseria Gonorrhoeae Organism_taxid: 485 Gene: Ygbp Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 1 21 1	R_factor 0.260 R_Free 0.317
crystal cell	length a length b length c angle alpha angle beta angle gamma 50.168 95.109 173.856 90.00 93.65 90.00
method	X-Ray Diffraction	resolution	2.35 Å
ligand		enzyme	Transferase E.C.2.7.7 BRENDA
note	1VGW is a representative structure
related structures	by homologous chain: 1VGZ
Gene Ontology	Chain Function Process Component F, A, D, C, E, 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] (200 Kb) [Save to disk] Biological Unit Coordinates (1vgw.pdb1.gz) 68 Kb Biological Unit Coordinates (1vgw.pdb2.gz) 68 Kb Biological Unit Coordinates (1vgw.pdb3.gz) 67 Kb CSU: Contacts of Structural Units for 1VGW Likely Quarternary Molecular Structure file(s) for 1VGW Structure Factors (766 Kb) Retrieve 1VGW in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1VGW from S2C, [Save to disk] Re-refined 1vgw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1VGW 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 1VGW

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 1VGW, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1vgwa_, region A [Jmol] [rasmolscript] [script source]     - Domain d1vgwb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1vgwc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1vgwd_, region D [Jmol] [rasmolscript] [script source]     - Domain d1vgwe_, region E [Jmol] [rasmolscript] [script source]     - Domain d1vgwf_, region F [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: [1vgw_A] [1vgw_D] [1vgw_F] [1vgw_B] [1vgw_E] [1vgw_C] [1vgw] SWISS-PROT database: [Q5F829] Domain organization of [ISPD_NEIG1] by SWISSPFAM

Other resources with information on 1VGW

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

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