1MDB Ligase date Aug 07, 2002
title Crystal Structure Of Dhbe In Complex With Dhb-Adenylate
authors J.J.May, N.Kessler, M.A.Marahiel, M.T.Stubbs
compound source
Molecule: 2,3-Dihydroxybenzoate-Amp Ligase
Chain: A
Synonym: Dhbe, Dihydroxybenzoic Acid-Activating Enzyme
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Strain: Atcc 21332
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: M15 Prep4
symmetry Space Group: P 31
R_factor 0.217 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.800 66.800 115.660 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.15 Å
ligand AMP, DBH, SO4 enzyme Ligase E.C.6.3.2 BRENDA
related structures by homologous chain: 1MDF
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases., May JJ, Kessler N, Marahiel MA, Stubbs MT, Proc Natl Acad Sci U S A 2002 Sep 17;99(19):12120-5. PMID:12221282
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (1mdb.pdb1.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 1MDB
  • CSU: Contacts of Structural Units for 1MDB
  • Likely Quarternary Molecular Structure file(s) for 1MDB
  • Retrieve 1MDB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1MDB from S2C, [Save to disk]
  • View 1MDB 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 1MDB
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1MDB, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1mdba_, region A [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: [1mdb_A] [1mdb]
  • SWISS-PROT database: [P40871]
  • Domain organization of [DHBE_BACSU] by SWISSPFAM
  • Other resources with information on 1MDB
  • Community annotation for 1MDB 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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