5HDP Hydrolase date Jan 05, 2016
title Hydrolase Stna Mutant - S185a
authors T.Qian
compound source
Molecule: Hydrolase
Chain: D, A, B, C, E, F, G
Engineered: Yes
Mutation: Yes
 Organism_scientific: Streptomyces Flocculus
Organism_taxid: 67300
Gene: Stna
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
Expression_system_strain: Bl21-Gold(De3)Plyss Ag
Expression_system_vector_type: Plasmid
symmetry Space Group: P 1
R_factor 0.244 R_Free 0.298
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.256 92.847 104.037 115.06 106.09 97.69
method X-Ray Diffractionresolution 2.90 Å
ligand STM enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, G, E, B


Primary referenceCrystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode., Qian T, Wo J, Zhang Y, Song Q, Feng G, Luo R, Lin S, Wu G, Chen HF, Sci Rep. 2017 Jan 11;7:40254. doi: 10.1038/srep40254. PMID:28074848
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (347 Kb) [Save to disk]
  • Biological Unit Coordinates (5hdp.pdb1.gz) 53 Kb
  • Biological Unit Coordinates (5hdp.pdb2.gz) 53 Kb
  • Biological Unit Coordinates (5hdp.pdb3.gz) 53 Kb
  • Biological Unit Coordinates (5hdp.pdb4.gz) 53 Kb
  • Biological Unit Coordinates (5hdp.pdb5.gz) 53 Kb
  • Biological Unit Coordinates (5hdp.pdb6.gz) 53 Kb
  • Biological Unit Coordinates (5hdp.pdb7.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 5HDP
  • CSU: Contacts of Structural Units for 5HDP
  • Structure Factors (1684 Kb)
  • Retrieve 5HDP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5HDP from S2C, [Save to disk]
  • Re-refined 5hdp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5HDP 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 5HDP
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5hdp_D] [5hdp_G] [5hdp] [5hdp_E] [5hdp_A] [5hdp_B] [5hdp_C] [5hdp_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5HDP
  • Community annotation for 5HDP at PDBWiki (http://pdbwiki.org)

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