3D1Y Hydrolase Hydrolase Inhibitor date May 06, 2008
title Crystal Structure Of Hiv-1 Mutant I54v And Inhibitor Saquina
authors F.Liu, I.T.Weber
compound source
Molecule: Hiv-1 Protease
Chain: A, B
Synonym: Retropepsin, Pr
Ec: 3.4.23.16
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus Type 1
Organism_common: Hiv-1
Organism_taxid: 11682
Gene: Gag-Pol
Expression_system: Escherichia Coli
symmetry Space Group: P 21 21 2
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.720 85.940 46.380 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.05 Å
ligand CL, NA, ROC BindingDB enzyme Hydrolase E.C.3.4.23.16 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceEffect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir., Liu F, Kovalevsky AY, Tie Y, Ghosh AK, Harrison RW, Weber IT, J Mol Biol. 2008 Aug 1;381(1):102-15. Epub 2008 Jul 1. PMID:18597780
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (3d1y.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 3D1Y
  • CSU: Contacts of Structural Units for 3D1Y
  • Likely Quarternary Molecular Structure file(s) for 3D1Y
  • Structure Factors (899 Kb)
  • Retrieve 3D1Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D1Y from S2C, [Save to disk]
  • Re-refined 3d1y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D1Y 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 3D1Y
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3D1Y, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d1y_B] [3d1y] [3d1y_A]
  • SWISS-PROT database: [P04587]
  • Domain organization of [POL_HV1B5] by SWISSPFAM
  • Other resources with information on 3D1Y
  • Community annotation for 3D1Y 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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