4YMD CL-K1 trimer bound to man(alpha1-2)man date
authors Wallis, R., Girija, U.Venkatraman., Gingras, A.R., Moody, P.C.E., Marshall, J.E.
compound source
symmetry
R_factor
R_Free 0.2640
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.87
ligand CA, GOL, MAN enzyme
Primary referenceMolecular basis of sugar recognition by collectin-K1 and the effects of mutations associated with 3MC syndrome., Girija UV, Furze CM, Gingras AR, Yoshizaki T, Ohtani K, Marshall JE, Wallis AK, Schwaeble WJ, El-Mezgueldi M, Mitchell DA, Moody PC, Wakamiya N, Wallis R, BMC Biol. 2015 Apr 17;13(1):27. PMID:25912189
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (319 Kb) [Save to disk]
  • Biological Unit Coordinates (4ymd.pdb1.gz) 156 Kb
  • Biological Unit Coordinates (4ymd.pdb2.gz) 155 Kb
  • LPC: Ligand-Protein Contacts for 4YMD
  • CSU: Contacts of Structural Units for 4YMD
  • Structure Factors (1259 Kb)
  • Retrieve 4YMD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YMD from S2C, [Save to disk]
  • Re-refined 4ymd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4YMD 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 4YMD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4YMD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ymd_F] [4ymd_C] [4ymd_D] [4ymd_B] [4ymd_A] [4ymd] [4ymd_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4YMD: [CLECT ] by SMART
    • Other resources with information on 4YMD
  • Community annotation for 4YMD at PDBWiki (http://pdbwiki.org)

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