3DOX Hydrolase date Jul 07, 2008
title X-Ray Structure Of Hiv-1 Protease In Situ Product Complex
authors M.V.Hosur, J.L.Ferrer, A.Das, V.Prashar, S.Bihani
compound source
Molecule: Hiv-1 Protease
Chain: A
Synonym: Pr160gag-Pol, Matrix Protein P17, Ma, Capsid Prote Ca, Spacer Peptide P2, Nucleocapsid Protein P7, Nc, Transfr Peptide, Tf, P6-Pol, P6, Protease, Retropepsin, Pr, Revers Transcriptaseribonuclease H, P66 Rt, P51 Rt, P15, Integras
Ec: 3.4.23.16
Engineered: Yes
Mutation: Yes
Other_details: Tethered Dimer Linked By Ggssg
Organism_scientific: Human Immunodeficiency Virus Type 1 (I Hxb2 Group M Subtype B);
Organism_common: Hiv-1, Hiv-1 M:B_hxb2r
Organism_taxid: 11706
Gene: Gag-Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: A Peptide Substrate-Sqny
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized.

Molecule: A Peptide Substrate-Piv
Chain: Q
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized.
symmetry Space Group: P 61
R_factor 0.197 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.380 62.380 82.000 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 Å
ligand
enzyme Hydrolase E.C.3.4.23.16 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceX-ray structure of HIV-1 protease in situ product complex., Bihani S, Das A, Prashar V, Ferrer JL, Hosur MV, Proteins. 2008 Aug 14. PMID:18704947
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (42 Kb) [Save to disk]
  • Biological Unit Coordinates (3dox.pdb1.gz) 37 Kb
  • CSU: Contacts of Structural Units for 3DOX
  • Likely Quarternary Molecular Structure file(s) for 3DOX
  • Structure Factors (101 Kb)
  • Retrieve 3DOX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DOX from S2C, [Save to disk]
  • Re-refined 3dox structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DOX 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 3DOX
  • 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 3DOX, from MSDmotif at EBI
  • Fold representative 3dox from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dox_Q] [3dox] [3dox_P] [3dox_A]
  • SWISS-PROT database: [P04585]
  • Domain organization of [POL_HV1H2] by SWISSPFAM
  • Other resources with information on 3DOX
  • Community annotation for 3DOX 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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