3B80

HIV-1 protease mutant I54V complexed with gem-diol-amine intermediate NLLTQI

Structural Biology Knowledgebase: 3B80 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Observed: 0.153

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3B80

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 22301.79

Macromolecule Entities
Molecule Chains Length Organism Details
Protease A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Fragment: UNP residues 501-599
Mutation: Q7K, L33I, I54V, L63I, C67A, C95A
Gene Name(s): gag-pol pol
peptide C 5 Human immunodeficiency virus 1 Fragment: self proteolytic product of HIV-1 protease

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000321 (GLN,ASN,LEU,ILE,LNT) C N-{(2S)-2-[(L-asparaginyl-L-leucyl)amino]-1,1-dihydroxy-4-methylpentyl}-L-threonyl-L-glutaminyl-L-isoleucine Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Observed: 0.153
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.44 α = 90.00
b = 86.02 β = 90.00
c = 46.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-10-31
  • Released Date: 2007-12-18
  • Deposition author(s): Chumanevich, A.A., Kovalevsky, A.Y., Weber, I.T.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4