1VPO Immune System date Nov 15, 2004
title Crystal Structure Analysis Of The Anti-Testosterone Fab In C With Testosterone
authors J.M.Valjakka, A.Hemminki, S.Niemi, H.Soderlund, K.Takkinen, J.Rou
compound source
Molecule: Anti-Testosterone (Light Chain)
Chain: L
Fragment: Fab77 Fragment
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rv308
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pkktac

Molecule: Anti-Testosterone (Heavy Chain)
Chain: H
Fragment: Fab77 Fragment
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rv308
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pkktac
symmetry Space Group: P 62
R_factor 0.211 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.252 82.252 120.059 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.15 Å
ligand TES enzyme
note 1VPO supersedes 1L7S
related structures by homologous chain: 1AXT, 1JGL
Primary referenceCrystal structure of an in vitro affinity- and specificity-matured anti-testosterone Fab in complex with testosterone. Improved affinity results from small structural changes within the variable domains., Valjakka J, Hemminki A, Niemi S, Soderlund H, Takkinen K, Rouvinen J, J Biol Chem 2002 Nov 15;277(46):44021-7. Epub 2002 Aug 23. PMID:12196551
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (1vpo.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (1vpo.pdb2.gz) 147 Kb
  • LPC: Ligand-Protein Contacts for 1VPO
  • CSU: Contacts of Structural Units for 1VPO
  • Likely Quarternary Molecular Structure file(s) for 1VPO
  • Structure Factors (178 Kb)
  • Retrieve 1VPO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VPO from S2C, [Save to disk]
  • Re-refined 1vpo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VPO 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 1VPO
  • 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 1VPO, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vpoh1, region H:1-118 [Jmol] [rasmolscript] [script source]
        - Domain d1vpoh2, region H:119-221 [Jmol] [rasmolscript] [script source]
        - Domain d1vpol1, region L:1-112 [Jmol] [rasmolscript] [script source]
        - Domain d1vpol2, region L:113-219 [Jmol] [rasmolscript] [script source]
  • Fold representative 1vpo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vpo] [1vpo_L] [1vpo_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 1VPO: [IG_like] [IGv ] by SMART
  • Other resources with information on 1VPO
  • Community annotation for 1VPO 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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