2AVV

Kinetics, stability, and structural changes in high resolution crystal structures of HIV-1 protease with drug resistant mutations L24I, I50V, and G73S

Structural Biology Knowledgebase: 2AVV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.140

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2AVV

Classification: HYDROLASE

Total Structure Weight: 44561.86

Macromolecule Entities
Molecule Chains Length Organism Details
Pol polyprotein A, B, D, E 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Fragment: RETROPEPSIN
Mutation: Q7K, L33I, L63I, C67A, G73S, 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

A, E 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)
ACY
Query on ACY

A, B, E ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B, D 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: 0.55 nM  BindingMOAD
Ki: 0.55 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.140
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 51.27 α = 90.00
b = 62.72 β = 98.15
c = 59.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-08-30
  • Released Date: 2006-01-24
  • Deposition author(s): Liu, F., Boross, P.I., Wang, Y.F., 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