1SDU

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

Structural Biology Knowledgebase: 1SDU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.141

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1SDU

Classification: HYDROLASE

Total Structure Weight: 22286.53

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, L90M, C95A
Details: complexed with indinavir
Gene Name(s): gag-pol

Small Molecules
Ligands 3 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)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.141
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 51.33 α = 90.00
b = 58.45 β = 90.00
c = 61.65 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