1SDV

Crystal structures of HIV protease V82A and L90M mutants reveal changes in indinavir binding site.

Structural Biology Knowledgebase: 1SDV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.160

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1SDV

Classification: HYDROLASE

Total Structure Weight: 22110.10

Macromolecule Entities
Molecule Chains Length Organism Details
protease RETROPEPSIN A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Mutation: Q7K, L33I, L63I, C67A, V82A, C95A
Details: complexed with indinavir
Gene Name(s): gag-pol

Small Molecules
Ligands 2 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)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MK1 IC50: 0.36 - 370 nM (92) BindingDB
Kd: 1.07 nM (92) BindingDB
Ki: 0.24 - 50 nM (92) BindingDB

Ki: 1.81 nM  BindingMOAD
Ki: 1.81 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.160
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 85.82 α = 90.00
b = 58.73 β = 90.00
c = 46.59 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-02-14
  • Released Date: 2004-05-25
  • Deposition author(s): Mahalingam, B., Wang, Y.-F., Boross, P.I., Tozser, J., Louis, J.M., Harrison, R.W., Weber, I.T.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4