2ZPK Immune System date Jul 16, 2008
title Crystal Structure Of P20.1 Fab Fragment In Complex With Its Peptide
authors T.Nogi, T.Sanagawa, J.Takagi
compound source
Molecule: Igg1-Lambda P20.1 Fab (Light Chain)
Chain: L, M
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Strain: Balbc

Molecule: Igg1-Lambda P20.1 Fab (Heavy Chain)
Chain: H, I
Fragment: Variable And Constant Region

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Strain: Balbc

Molecule: Proteinase-Activated Receptor 4
Chain: P, Q
Fragment: Unp Residues 46-53
Synonym: Par-4, Thrombin Receptor-Like 3, Coagulation Facto Receptor-Like 3;
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occurs In The N-Terminal Regio Human Protease-Activated Receptor 4.
symmetry Space Group: P 1
R_factor 0.172 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.045 65.271 85.030 99.93 93.50 96.46
method X-Ray Diffractionresolution 1.80 Å
ligand GOL, PCA enzyme
Primary referenceNovel affinity tag system using structurally defined antibody-tag interaction: application to single-step protein purification., Nogi T, Sangawa T, Tabata S, Nagae M, Tamura-Kawakami K, Beppu A, Hattori M, Yasui N, Takagi J, Protein Sci. 2008 Dec;17(12):2120-6. Epub 2008 Sep 11. PMID:18787202
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]
  • Biological Unit Coordinates (2zpk.pdb1.gz) 77 Kb
  • Biological Unit Coordinates (2zpk.pdb2.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 2ZPK
  • CSU: Contacts of Structural Units for 2ZPK
  • Structure Factors (554 Kb)
  • Retrieve 2ZPK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ZPK from S2C, [Save to disk]
  • Re-refined 2zpk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ZPK 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 2ZPK
  • 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 2ZPK, from MSDmotif at EBI
  • Fold representative 2zpk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2zpk_L] [2zpk_M] [2zpk_P] [2zpk_I] [2zpk_Q] [2zpk] [2zpk_H]
  • SWISS-PROT database: [Q96RI0]
  • Domain organization of [PAR4_HUMAN] by SWISSPFAM
  • Domains found in 2ZPK: [IG_like] [IGv ] by SMART
  • Other resources with information on 2ZPK
  • Community annotation for 2ZPK 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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