2RKF

HIV-1 PR resistant mutant + LPV

Structural Biology Knowledgebase: 2RKF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.189

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2RKF

Classification: HYDROLASE

Total Structure Weight: 22572.61

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEASE RETROPEPSIN A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Mutation: I13V, G16A, K20M, N37S, I46V, L54M, P63L, L93I
Gene Name(s): pol

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AB1
Query on AB1

A N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]- 3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2- OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE
ABT-378, LOPINAVIR (Synonym)
C37 H48 N4 O5
KJHKTHWMRKYKJE-SUGCFTRWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
AB1 N/A in BindingDB
Ki: 0.83 nM  BindingMOAD
Ki: 0.83 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.189
  • Space Group: P 61
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 61.96 α = 90.00
b = 61.96 β = 90.00
c = 84.11 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-10-16
  • Released Date: 2008-08-05
  • Deposition author(s): Rezacova, P., Brynda, J., Kozisek, M., Saskova, K.G., Konvalinka, J.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4