1NYT Oxidoreductase date Feb 13, 2003
title Shikimate Dehydrogenase Aroe Complexed With Nadp+
authors A.W.Roszak, A.J.Lapthorn
compound source
Molecule: Shikimate 5-Dehydrogenase
Chain: A, B, C, D
Ec: 1.1.1.25
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Aroe
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ab2834
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptb361
symmetry Space Group: C 1 2 1
R_factor 0.132 R_Free 0.169
crystal
cell
length a length b length c angle alpha angle beta angle gamma
110.524 140.019 102.712 90.00 122.07 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand DTV, NAP, SO4 enzyme Oxidoreductase E.C.1.1.1.25 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructures of shikimate dehydrogenase AroE and its Paralog YdiB. A common structural framework for different activities., Michel G, Roszak AW, Sauve V, Maclean J, Matte A, Coggins JR, Cygler M, Lapthorn AJ, J Biol Chem 2003 May 23;278(21):19463-72. PMID:12637497
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (397 Kb) [Save to disk]
  • Biological Unit Coordinates (1nyt.pdb1.gz) 389 Kb
  • Biological Unit Coordinates (1nyt.pdb2.gz) 775 Kb
  • Biological Unit Coordinates (1nyt.pdb3.gz) 772 Kb
  • LPC: Ligand-Protein Contacts for 1NYT
  • CSU: Contacts of Structural Units for 1NYT
  • Likely Quarternary Molecular Structure file(s) for 1NYT
  • Structure Factors (1496 Kb)
  • Retrieve 1NYT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NYT from S2C, [Save to disk]
  • Re-refined 1nyt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1NYT 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 1NYT
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Conformational Epitope Prediction for 1NYT 1NYTA 1NYTB 1NYTC 1NYTD from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1NYT, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nyta2, region A:1-101 [Jmol] [rasmolscript] [script source]
        - Domain d1nyta1, region A:102-271 [Jmol] [rasmolscript] [script source]
        - Domain d1nytb2, region B:1-101 [Jmol] [rasmolscript] [script source]
        - Domain d1nytb1, region B:102-271 [Jmol] [rasmolscript] [script source]
        - Domain d1nytc2, region C:1-101 [Jmol] [rasmolscript] [script source]
        - Domain d1nytc1, region C:102-269 [Jmol] [rasmolscript] [script source]
        - Domain d1nytd2, region D:1-101 [Jmol] [rasmolscript] [script source]
        - Domain d1nytd1, region D:102-270 [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: [1nyt_C] [1nyt_D] [1nyt_A] [1nyt_B] [1nyt]
  • SWISS-PROT database: [P15770]
  • Domain organization of [AROE_ECOLI] by SWISSPFAM
    • Other resources with information on 1NYT
  • Community annotation for 1NYT 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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