2AVS

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: 2AVS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.141
  • R-Value Work: 0.107

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2AVS

Classification: HYDROLASE

Total Structure Weight: 22671.73

Macromolecule Entities
Molecule Chains Length Organism Details
Pol polyprotein A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Fragment: retropepsin
Mutation: Q7K, L33I, I50V, L63I, C67A, C95A
Details: COMPLEXED WITH INDINAVIR
Gene Name(s): gag-pol

Small Molecules
Ligands 5 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)
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

B DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

B ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
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: 27 nM  BindingMOAD
Ki: 27.0 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.141
  • R-Value Work: 0.107
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 51.34 α = 90.00
b = 58.43 β = 90.00
c = 60.97 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