1NVD Lyase date Feb 03, 2003
title Crystal Structure Of 3-Dehydroquinate Synthase (Dhqs) In Com Zn2+ And Carbaphosphonate
authors C.E.Nichols, J.Ren, H.K.Lamb, A.R.Hawkins, D.K.Stammers
compound source
Molecule: 3-Dehydroquinate Synthase
Chain: A, B
Synonym: Dhqs
Ec: 4.2.3.4
Engineered: Yes
Organism_scientific: Emericella Nidulans
Organism_taxid: 162425
Gene: Aroma
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Glw38 (Arob-)
Expression_system_vector_type: Plasmid
Expression_system_vector: Ptrc99a
Expression_system_plasmid: Ptr51
symmetry Space Group: P 21 21 21
R_factor 0.196 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
64.030 70.030 197.630 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.51 Å
ligand CL, CRB, ZN enzyme Lyase E.C.4.2.3.4 BRENDA
related structures by homologous chain: 1NR5, 1NVE
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceLigand-induced conformational changes and a mechanism for domain closure in Aspergillus nidulans dehydroquinate synthase., Nichols CE, Ren J, Lamb HK, Hawkins AR, Stammers DK, J Mol Biol 2003 Mar 14;327(1):129-44. PMID:12614613
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (1nvd.pdb1.gz) 132 Kb
  • LPC: Ligand-Protein Contacts for 1NVD
  • CSU: Contacts of Structural Units for 1NVD
  • Likely Quarternary Molecular Structure file(s) for 1NVD
  • Structure Factors (240 Kb)
  • Retrieve 1NVD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NVD from S2C, [Save to disk]
  • Re-refined 1nvd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1NVD 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 1NVD
  • 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 1NVD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nvda_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1nvdb_, 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: [1nvd] [1nvd_B] [1nvd_A]
  • SWISS-PROT database: [P07547]
  • Domain organization of [ARO1_EMENI] by SWISSPFAM
  • Other resources with information on 1NVD
  • Community annotation for 1NVD 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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