4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 date 2012-08-15
authors Karatas, H., Townsend, E.C., Chen, Y., Bernard, D., Cao, F., Liu, L., Lei, M., Dou, Y., Wang, S.
compound source
symmetry
R_factor
R_Free 0.2258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.39
ligand 0XL, 0XM, AC5, ALQ enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceHigh-affinity, small-molecule peptidomimetic inhibitors of MLL1/WDR5 protein-protein interaction., Karatas H, Townsend EC, Cao F, Chen Y, Bernard D, Liu L, Lei M, Dou Y, Wang S, J Am Chem Soc. 2013 Jan 16;135(2):669-82. doi: 10.1021/ja306028q. Epub 2012 Dec, 27. PMID:23210835
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (389 Kb) [Save to disk]
  • Biological Unit Coordinates (4gm3.pdb1.gz) 54 Kb
  • Biological Unit Coordinates (4gm3.pdb2.gz) 53 Kb
  • Biological Unit Coordinates (4gm3.pdb3.gz) 53 Kb
  • Biological Unit Coordinates (4gm3.pdb4.gz) 53 Kb
  • Biological Unit Coordinates (4gm3.pdb5.gz) 53 Kb
  • Biological Unit Coordinates (4gm3.pdb6.gz) 53 Kb
  • Biological Unit Coordinates (4gm3.pdb7.gz) 53 Kb
  • Biological Unit Coordinates (4gm3.pdb8.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 4GM3
  • CSU: Contacts of Structural Units for 4GM3
  • Structure Factors (267 Kb)
  • Retrieve 4GM3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GM3 from S2C, [Save to disk]
  • Re-refined 4gm3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4GM3 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 4GM3
  • 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
  • 3D motif for 4GM3, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gm3_E] [4gm3_B] [4gm3_M] [4gm3_H] [4gm3_N] [4gm3] [4gm3_F] [4gm3_G] [4gm3_K] [4gm3_P] [4gm3_L] [4gm3_I] [4gm3_O] [4gm3_A] [4gm3_C] [4gm3_J] [4gm3_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4GM3: [WD40 ] by SMART
    • Other resources with information on 4GM3
  • Community annotation for 4GM3 at PDBWiki (http://pdbwiki.org)

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