5D5C Hydrolase date Aug 10, 2015
title In Meso In Situ Serial X-Ray Crystallography Structure Of Ly 100 K
authors C.Y.Huang, V.Olieric, K.Diederichs, M.Wang, M.Caffrey
compound source
Molecule: Lysozyme C
Chain: A
Synonym: 1,4-Beta-N-Acetylmuramidase C,Allergen Gal D Iv
Ec: 3.2.1.17
 Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
symmetry Space Group: P 43 21 2
R_factor 0.183 R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
79.090 79.090 38.290 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand ACY, BR, NA, PE5 enzyme Hydrolase E.C.3.2.1.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceIn meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures., Huang CY, Olieric V, Ma P, Howe N, Vogeley L, Liu X, Warshamanage R, Weinert T, Panepucci E, Kobilka B, Diederichs K, Wang M, Caffrey M, Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):93-112. doi:, 10.1107/S2059798315021683. Epub 2016 Jan 1. PMID:26894538
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (28 Kb) [Save to disk]
  • Biological Unit Coordinates (5d5c.pdb1.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 5D5C
  • CSU: Contacts of Structural Units for 5D5C
  • Structure Factors (125 Kb)
  • Retrieve 5D5C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D5C from S2C, [Save to disk]
  • Re-refined 5d5c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5D5C 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 5D5C
  • 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: [5d5c_A] [5d5c]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5D5C: [LYZ1 ] by SMART
    • Other resources with information on 5D5C
  • Community annotation for 5D5C at PDBWiki (http://pdbwiki.org)

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