2NMY Hydrolase Hydrolase Inhibitor date Oct 23, 2006
title Crystal Structure Analysis Of Hiv-1 Protease Mutant V82a Wit Inhibitor Saquinavir
authors Y.Tie, A.Y.Kovalevsky, P.Boross, Y.F.Wang, A.K.Ghosh, J.Tozser, R.W.Harrison, I.T.Weber
compound source
Molecule: Protease
Chain: A, B
Synonym: Retropepsin, Pr
Ec: 3.4.23.16
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Gene: Gag
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
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
59.988 87.464 47.190 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.10 Å
ligand CL, NA, ROC, SO4 BindingDB enzyme Hydrolase E.C.3.4.23.16 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceAtomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir., Tie Y, Kovalevsky AY, Boross P, Wang YF, Ghosh AK, Tozser J, Harrison RW, Weber IT, Proteins. 2007 Jan 22;67(1):232-242. PMID:17243183
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (85 Kb) [Save to disk]
  • Biological Unit Coordinates (2nmy.pdb1.gz) 79 Kb
  • LPC: Ligand-Protein Contacts for 2NMY
  • CSU: Contacts of Structural Units for 2NMY
  • Likely Quarternary Molecular Structure file(s) for 2NMY
  • Structure Factors (882 Kb)
  • Retrieve 2NMY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NMY from S2C, [Save to disk]
  • Re-refined 2nmy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2NMY 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 2NMY
  • 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 2NMY, from MSDmotif at EBI
  • Fold representative 2nmy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2nmy_B] [2nmy] [2nmy_A]
  • SWISS-PROT database: [P04587]
  • Domain organization of [POL_HV1B5] by SWISSPFAM
  • Other resources with information on 2NMY
  • Community annotation for 2NMY 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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