2NPH Hydrolase date Oct 27, 2006
title Crystal Structure Of Hiv1 Protease In Situ Product Complex
authors M.V.Hosur, A.Das, V.Prashar
compound source
Molecule: Protease Retropepsin
Chain: A, B
Synonym: Hiv-1 Protease
Ec: 3.4.23.16
Engineered: Yes
Other_details: Observation Of A Low Barrier Hydrogen Bond B Catalytic Aspartates;
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Gene: Pol
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a

Molecule: Tetrapeptide Fragment
Chain: S
Engineered: Yes

Synthetic: Yes

Molecule: Pentapeptide Fragment
Chain: T
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 61
R_factor 0.214 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.030 62.030 81.780 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.65 Å
ligand
enzyme Hydrolase E.C.3.4.23.16 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of HIV-1 protease in situ product complex and observation of a low-barrier hydrogen bond between catalytic aspartates., Das A, Prashar V, Mahale S, Serre L, Ferrer JL, Hosur MV, Proc Natl Acad Sci U S A. 2006 Dec 5;103(49):18464-9. Epub 2006 Nov 20. PMID:17116869
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk]
  • Biological Unit Coordinates (2nph.pdb1.gz) 36 Kb
  • CSU: Contacts of Structural Units for 2NPH
  • Likely Quarternary Molecular Structure file(s) for 2NPH
  • Retrieve 2NPH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NPH from S2C, [Save to disk]
  • View 2NPH 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 2NPH
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2NPH, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2nph_B] [2nph_T] [2nph_S] [2nph_A] [2nph]
  • SWISS-PROT database: [P04585]
  • Domain organization of [POL_HV1H2] by SWISSPFAM
  • Other resources with information on 2NPH
  • Community annotation for 2NPH 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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