4DL1 Crystal Structure of human Myeloperoxidase with covalent thioxanthine analog date
authors Vajdos, F., Varghese, A.
compound source
symmetry
R_factor
R_Free 0.24617
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.00
ligand 0KY, BMA, CA, CL, CSO, FUC, HEM, MAN, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, N, K, E, M, C, L, A, J, O, P, B, H, D, I, G


Primary referenceDeconstruction of Activity-Dependent Covalent Modification of Heme in Human Neutrophil Myeloperoxidase by Multistage Mass Spectrometry (MS(4))., Geoghegan KF, Varghese AH, Feng X, Bessire AJ, Conboy JJ, Ruggeri RB, Ahn K, Spath SN, Filippov SV, Conrad SJ, Carpino PA, Guimaraes CR, Vajdos FF, Biochemistry. 2012 Mar 13;51(10):2065-77. Epub 2012 Mar 1. PMID:22352991
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1634 Kb) [Save to disk]
  • Biological Unit Coordinates (4dl1.pdb1.gz) 413 Kb
  • Biological Unit Coordinates (4dl1.pdb2.gz) 409 Kb
  • Biological Unit Coordinates (4dl1.pdb3.gz) 406 Kb
  • Biological Unit Coordinates (4dl1.pdb4.gz) 413 Kb
  • Biological Unit Coordinates (4dl1.pdb5.gz) 211 Kb
  • Biological Unit Coordinates (4dl1.pdb6.gz) 212 Kb
  • Biological Unit Coordinates (4dl1.pdb7.gz) 210 Kb
  • Biological Unit Coordinates (4dl1.pdb8.gz) 209 Kb
  • Biological Unit Coordinates (4dl1.pdb9.gz) 207 Kb
  • LPC: Ligand-Protein Contacts for 4DL1
  • CSU: Contacts of Structural Units for 4DL1
  • Structure Factors (4678 Kb)
  • Retrieve 4DL1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DL1 from S2C, [Save to disk]
  • Re-refined 4dl1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4DL1 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 4DL1
  • 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 4DL1, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dl1_D] [4dl1] [4dl1_F] [4dl1_O] [4dl1_P] [4dl1_I] [4dl1_G] [4dl1_J] [4dl1_H] [4dl1_M] [4dl1_E] [4dl1_B] [4dl1_A] [4dl1_L] [4dl1_N] [4dl1_C] [4dl1_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4DL1
  • Community annotation for 4DL1 at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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