2PK5 Hydrolase Hydrolase Inhibitor date Apr 17, 2007
title Crystal Structure Of Hiv-1 Protease (Q7k, L33i, L63i ) In Co Kni-10075
authors A.A.Armstrong, V.Lafont, Y.Kiso, E.Freire, L.M.Amzel
compound source
Molecule: Protease
Chain: A, B
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Strain: Subtype B
Gene: Gag-Pol
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24a+
symmetry Space Group: P 21 21 2
R_factor 0.160 R_Free 0.200
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.842 85.991 46.210 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand 075, GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCompensating enthalpic and entropic changes hinder binding affinity optimization., Lafont V, Armstrong AA, Ohtaka H, Kiso Y, Mario Amzel L, Freire E, Chem Biol Drug Des. 2007 Jun;69(6):413-22. PMID:17581235
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (2pk5.pdb1.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 2PK5
  • CSU: Contacts of Structural Units for 2PK5
  • Likely Quarternary Molecular Structure file(s) for 2PK5
  • Retrieve 2PK5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PK5 from S2C, [Save to disk]
  • View 2PK5 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 2PK5
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2PK5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pk5_B] [2pk5_A] [2pk5]
  • SWISS-PROT database: [P03367]
  • Domain organization of [POL_HV1BR] by SWISSPFAM
  • Other resources with information on 2PK5
  • Community annotation for 2PK5 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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