1V5W Recombination date Nov 26, 2003
title Crystal Structure Of The Human Dmc1 Protein
authors T.Kinebuchi, W.Kagawa, R.Enomoto, S.Ikawa, T.Shibata, H.Kurumizak S.Yokoyama, Riken Structural Genomicsproteomics Initiative
compound source
Molecule: Meiotic Recombination Protein Dmc1lim15 Homolog
Chain: A, B
Synonym: Dmc1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dmc1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15b
symmetry Space Group: I 4 2 2
R_factor 0.294 R_Free 0.346
crystal
cell
length a length b length c angle alpha angle beta angle gamma
124.091 124.091 218.830 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmc1., Kinebuchi T, Kagawa W, Enomoto R, Tanaka K, Miyagawa K, Shibata T, Kurumizaka H, Yokoyama S, Mol Cell 2004 May 7;14(3):363-74. PMID:15125839
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (1v5w.pdb1.gz) 304 Kb
  • Biological Unit Coordinates (1v5w.pdb2.gz) 607 Kb
  • CSU: Contacts of Structural Units for 1V5W
  • Likely Quarternary Molecular Structure file(s) for 1V5W
  • Structure Factors (130 Kb)
  • Retrieve 1V5W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1V5W from S2C, [Save to disk]
  • Re-refined 1v5w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1V5W 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 1V5W
  • 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 1V5W, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1v5wa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1v5wb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1v5w from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1v5w] [1v5w_B] [1v5w_A]
  • SWISS-PROT database: [Q14565]
  • Domain organization of [DMC1_HUMAN] by SWISSPFAM
  • Domain found in 1V5W: [AAA ] by SMART
  • Other resources with information on 1V5W
  • Community annotation for 1V5W 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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