3KDM Crystal Structure of Human Anti-steroid Fab 5F2 in Complex with Testosterone date
authors Niemi, M.H., Rouvinen, J.
compound source
R_Free 0.208
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.50
ligand PCA, TES enzyme
Primary referenceThe testosterone binding mechanism of an antibody derived from a naive human scFv library., Niemi MH, Takkinen K, Amundsen LK, Soderlund H, Rouvinen J, Hoyhtya M, J Mol Recognit. 2011 Mar-Apr;24(2):209-19. doi: 10.1002/jmr.1039. PMID:21360611
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (156 Kb) [Save to disk]
  • Biological Unit Coordinates (3kdm.pdb1.gz) 77 Kb
  • Biological Unit Coordinates (3kdm.pdb2.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 3KDM
  • CSU: Contacts of Structural Units for 3KDM
  • Structure Factors (1076 Kb)
  • Retrieve 3KDM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KDM from S2C, [Save to disk]
  • Re-refined 3kdm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KDM 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 3KDM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3KDM, from MSDmotif at EBI
  • Fold representative 3kdm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kdm_B] [3kdm_L] [3kdm_A] [3kdm_H] [3kdm]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3KDM: [IG_like] [IGv ] by SMART
  • Other resources with information on 3KDM
  • Community annotation for 3KDM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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