4NVD Predicting protein conformational response in prospective ligand discovery. date 2013-12-05
authors Fischer, M., Fraser, J.S.
compound source
symmetry
R_factor
R_Free 0.1525
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.30
ligand 1LQ, HEM enzyme
Gene SCRG
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceIncorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery., Fischer M, Coleman RG, Fraser JS, Shoichet BK, Nat Chem. 2014 Jul;6(7):575-83. doi: 10.1038/nchem.1954. Epub 2014 May 25. PMID:24950326
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (129 Kb) [Save to disk]
  • Biological Unit Coordinates (4nvd.pdb1.gz) 124 Kb
  • LPC: Ligand-Protein Contacts for 4NVD
  • CSU: Contacts of Structural Units for 4NVD
  • Structure Factors (1037 Kb)
  • Retrieve 4NVD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NVD from S2C, [Save to disk]
  • Re-refined 4nvd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4NVD 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 4NVD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4NVD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nvd_A] [4nvd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4NVD
  • Community annotation for 4NVD at PDBWiki (http://pdbwiki.org)

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