2OTT Immune System date Feb 09, 2007
title Crystal Structure Of Cd5_diii
authors B.Rodamilans
compound source
Molecule: T-Cell Surface Glycoprotein Cd5
Chain: X, Y
Fragment: Cd5_diii
Synonym: Lymphocyte Antigen T1leu- 1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: B-Lymphocyte
Gene: Cd5, Leu1
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek-293ebna
Expression_system_tissue: Kidney Cells
Expression_system_plasmid: Pcep-Pu
symmetry Space Group: P 41 2 2
R_factor 0.216 R_Free 0.259
length a length b length c angle alpha angle beta angle gamma
74.161 74.161 128.990 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
X, Y

Primary referenceCrystal structure of the third extracellular domain of CD5 reveals the fold of a group B scavenger cysteine-rich receptor domain., Rodamilans B, Munoz IG, Bragado-Nilsson E, Sarrias MR, Padilla O, Blanco FJ, Lozano F, Montoya G, J Biol Chem. 2007 Feb 23;. PMID:17322294
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (37 Kb) [Save to disk]
  • Biological Unit Coordinates (2ott.pdb1.gz) 16 Kb
  • Biological Unit Coordinates (2ott.pdb2.gz) 16 Kb
  • CSU: Contacts of Structural Units for 2OTT
  • Likely Quarternary Molecular Structure file(s) for 2OTT
  • Structure Factors (190 Kb)
  • Retrieve 2OTT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OTT from S2C, [Save to disk]
  • Re-refined 2ott structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OTT 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 2OTT
  • 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 2OTT, from MSDmotif at EBI
  • Fold representative 2ott from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ott] [2ott_X] [2ott_Y]
  • SWISS-PROT database: [P06127]
  • Domain organization of [CD5_HUMAN] by SWISSPFAM
  • Domain found in 2OTT: [SR ] by SMART
  • Other resources with information on 2OTT
  • Community annotation for 2OTT 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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