1VHA Lyase date Dec 01, 2003
title Crystal Structure Of 2c-Methyl-D-Erythritol 2,4-Cyclodiphosp Synthase
authors Structural Genomix
compound source
Molecule: 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synt
Chain: A, B, C, D, E, F
Synonym: Mecps, Mecdp-Synthase
Ec: 4.6.1.12
Engineered: Yes
Organism_scientific: Haemophilus Influenzae
Organism_taxid: 727
Gene: Ispf, Hi0671
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: I 41
R_factor 0.244 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.715 104.715 195.864 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand ACY, MN, MSE, POP enzyme Lyase E.C.4.6.1.12 BRENDA
related structures by homologous chain: 1JY8, 1VH8
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, 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] (152 Kb) [Save to disk]
  • Biological Unit Coordinates (1vha.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (1vha.pdb2.gz) 74 Kb
  • Biological Unit Coordinates (1vha.pdb3.gz) 287 Kb
  • LPC: Ligand-Protein Contacts for 1VHA
  • CSU: Contacts of Structural Units for 1VHA
  • Likely Quarternary Molecular Structure file(s) for 1VHA
  • Structure Factors (501 Kb)
  • Retrieve 1VHA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VHA from S2C, [Save to disk]
  • Re-refined 1vha structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VHA 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 1VHA
  • 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 1VHA, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vhaa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1vhab_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1vhac_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1vhad_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1vhae_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1vhaf_, 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: [1vha] [1vha_E] [1vha_C] [1vha_B] [1vha_A] [1vha_D] [1vha_F]
  • SWISS-PROT database: [P44815]
  • Domain organization of [ISPF_HAEIN] by SWISSPFAM
  • Other resources with information on 1VHA
  • Community annotation for 1VHA 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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