3K05 Protein Binding date Sep 24, 2009
title The Crystal Structure Of Mdc1 Brct T2067d In Complex With A Recognition Tetrapeptide With An Amidated C-Terminus
authors S.J.Campbell, R.A.Edwards, J.N.Glover
compound source
Molecule: Mediator Of Dna Damage Checkpoint Protein 1
Chain: A, B
Fragment: Brct Domain (Unp Residues 1892 To 2089)
Synonym: Nuclear Factor With Brct Domains 1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kiaa0170, Mdc1, Nfbd1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Gold
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pkm596

Molecule: Phospho Peptide
Chain: C, D
Engineered: Yes

Synthetic: Yes
Organism_taxid: 9606
Other_details: This Sequence Occurs Naturally In Humans. Th Is Chemically Synthesized.
symmetry Space Group: P 21 21 21
R_factor 0.182 R_Free 0.202
length a length b length c angle alpha angle beta angle gamma
55.642 74.580 103.408 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.33 Å
ligand GOL, NH2, SEP enzyme
Primary referenceComparison of the structures and peptide binding specificities of the BRCT domains of MDC1 and BRCA1., Campbell SJ, Edwards RA, Glover JN, Structure. 2010 Feb 10;18(2):167-76. PMID:20159462
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]
  • Biological Unit Coordinates (3k05.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (3k05.pdb2.gz) 76 Kb
  • LPC: Ligand-Protein Contacts for 3K05
  • CSU: Contacts of Structural Units for 3K05
  • Structure Factors (1392 Kb)
  • Retrieve 3K05 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3K05 from S2C, [Save to disk]
  • Re-refined 3k05 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3K05 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 3K05
  • 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
  • 3D motif for 3K05, from MSDmotif at EBI
  • Fold representative 3k05 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3k05_C] [3k05_D] [3k05] [3k05_A] [3k05_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3K05: [BRCT ] by SMART
  • Other resources with information on 3K05
  • Community annotation for 3K05 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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