1D4K

HIV-1 PROTEASE COMPLEXED WITH A MACROCYCLIC PEPTIDOMIMETIC INHIBITOR

Structural Biology Knowledgebase: 1D4K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.212

Literature

Macromolecules
Sequence Display for 1D4K

Classification: HYDROLASE

Total Structure Weight: 22422.60

Macromolecule Entities
Molecule Chains Length Organism Details
HIV-1 PROTEASE A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Mutation: Q7K, L33I, C67X, C95X
Gene Name(s): gag-pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PI8
Query on PI8

A N-13-[(10S,13S)-9,12-DIOXO-10-(2-BUTYL)-2- OXA-8,11-DIAZABICYCLO [13.2.2] NONADECA-15,17,18- TRIENE] (2R)-BENZYL-(4S)-HYDROXY-5-AMINOPENTANOIC (1R)- HYDROXY-(2S)-INDANEAMIDE
MACROCYCLIC PEPTIDOMIMETIC INHIBITOR 8 (Synonym)
C41 H54 N4 O6
ZXUOAWXMXWTRGE-ZKQACQBYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PI8 N/A in BindingDB
Ki: 0.6 nM  BindingMOAD
Ki: 0.6 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
ABA
Query on ABA
A, B L-PEPTIDE LINKING C4 H9 N O2 ALA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.212
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 51.82 α = 90.00
b = 58.92 β = 90.00
c = 61.86 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-10-04
  • Released Date: 2000-10-11
  • Deposition author(s): Tyndall, J.D., Reid, R.C., Tyssen, D.P., Jardine, D.K., Todd, B., Passmore, M., March, D.R., Pattenden, L.K., Alewood, D., Hu, S.H., Alewood, P.F., Birch, C.J., Martin, J.L., Fairlie, D.P.

Revision History

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