5M9N Structural Protein date Nov 01, 2016
title Crystal Structure Of Human Tdrd1 Extended Tudor Domain In Co A Symmetrically Dimethylated E2f Peptide
authors C.Tallant, P.Savitsky, J.Moehlenbrink, C.Chan, G.Nunez-Alonso, J. F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, O.Fedorov, Thangue, S.Knapp, Structural Genomics Consortium (Sgc)
compound source
Molecule: Tudor Domain-Containing Protein 1
Chain: A, B
Synonym: Cancertestis Antigen 41.1,Ct41.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tdrd1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: E2f Peptide
Chain: C
Engineered: Yes
Other_details: 2mr: Dimethylated Arginine

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 1
R_factor 0.212 R_Free 0.260
length a length b length c angle alpha angle beta angle gamma
42.910 52.962 59.619 64.94 88.85 67.67
method X-Ray Diffractionresolution 1.95 Å
ligand 2MR, EDO enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (5m9n.pdb1.gz) 69 Kb
  • Biological Unit Coordinates (5m9n.pdb2.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 5M9N
  • CSU: Contacts of Structural Units for 5M9N
  • Structure Factors (688 Kb)
  • Retrieve 5M9N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5M9N from S2C, [Save to disk]
  • Re-refined 5m9n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5M9N 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 5M9N
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5m9n from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5m9n_A] [5m9n] [5m9n_B] [5m9n_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5M9N: [TUDOR ] by SMART
  • Other resources with information on 5M9N
  • Community annotation for 5M9N at PDBWiki (http://pdbwiki.org)

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