2PY2 Antifreeze Protein date May 15, 2007
title Structure Of Herring Type II Antifreeze Protein
authors Y.Liu, Z.Li, Q.Lin, J.Seetharaman, J.Sivaraman, C.L.Hew
compound source
Molecule: Antifreeze Protein Type II
Chain: A, B, C, D, E, F
Engineered: Yes
Organism_scientific: Clupea Harengus
Organism_common: Atlantic Herring
Organism_taxid: 7950
Gene: Hafp
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgapz Alpha A
symmetry Space Group: P 21 21 21
R_factor 0.209 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
31.279 146.415 192.406 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand CA enzyme
note 2PY2 is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceStructure and Evolutionary Origin of Ca-Dependent Herring Type II Antifreeze Protein., Liu Y, Li Z, Lin Q, Kosinski J, Seetharaman J, Bujnicki JM, Sivaraman J, Hew CL, PLoS ONE. 2007 Jun 20;2:e548. PMID:17579720
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (2py2.pdb1.gz) 24 Kb
  • Biological Unit Coordinates (2py2.pdb2.gz) 25 Kb
  • Biological Unit Coordinates (2py2.pdb3.gz) 25 Kb
  • Biological Unit Coordinates (2py2.pdb4.gz) 25 Kb
  • Biological Unit Coordinates (2py2.pdb5.gz) 25 Kb
  • Biological Unit Coordinates (2py2.pdb6.gz) 25 Kb
  • LPC: Ligand-Protein Contacts for 2PY2
  • CSU: Contacts of Structural Units for 2PY2
  • Likely Quarternary Molecular Structure file(s) for 2PY2
  • Structure Factors (679 Kb)
  • Retrieve 2PY2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PY2 from S2C, [Save to disk]
  • Re-refined 2py2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2PY2 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 2PY2
  • 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
  • 3D motif for 2PY2, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2py2_E] [2py2_D] [2py2_F] [2py2_C] [2py2_B] [2py2] [2py2_A]
  • SWISS-PROT database: [Q91992]
  • Domain organization of [Q91992_CLUHA] by SWISSPFAM
  • Domain found in 2PY2: [CLECT ] by SMART
  • Other resources with information on 2PY2
  • Community annotation for 2PY2 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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