2B7Z

Structure of HIV-1 protease mutant bound to indinavir

Structural Biology Knowledgebase: 2B7Z SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2B7Z

Classification: VIRAL PROTEIN

Total Structure Weight: 22277.40

Macromolecule Entities
Molecule Chains Length Organism Details
HIV-1 protease A, B 99 Human immunodeficiency virus 1 Mutation: K20R, V32I, L33F, M36I, M46I, L63P, A71V, V82A, I84V, L90M
Gene Name(s): gag-pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MK1
Query on MK1

B N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)- 4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY- 2(R)-PHENYLMETHYLPENTANAMIDE
INDINAVIR (Synonym)
C36 H47 N5 O4
CBVCZFGXHXORBI-PXQQMZJSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MK1 IC50: 0.36 - 370 nM (85 - 88) BindingDB
Kd: 1.07 nM (88) BindingDB
Ki: 0.052 - 481 nM (85 - 98) BindingDB
ΔG: -63.1 - -31.8 kJ/mol (85 - 90) BindingDB
ΔH: -31.8 - 51 kJ/mol (85 - 90) BindingDB
-TΔS: -82.8 - -5.8 kJ/mol (85 - 90) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.216
  • Space Group: P 61
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 61.83 α = 90.00
b = 61.83 β = 90.00
c = 84.03 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-10-05
  • Released Date: 2006-11-14
  • Deposition author(s): Clemente, J.C., Stow, L.R., Janka, L.K., Jeung, J.A., Desai, K.A., Govindasamy, L., Agbandje-McKenna, M., McKenna, R., Goodenow, M.M., Dunn, B.M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values