1M0B

HIV-1 protease in complex with an ethyleneamine inhibitor

Structural Biology Knowledgebase: 1M0B SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 1M0B

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 22387.63

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEASE RETROPEPSIN A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
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
0ZQ
Query on 0ZQ

B N-{(3S)-3-[(tert-butoxycarbonyl)amino]-4- phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl- L-phenylalaninamide
C38 H49 N5 O7
CBWQRQVEXJTNOT-ZLESDFJESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0ZQ N/A in BindingDB
Ki: 1.53 nM  BindingMOAD
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000383
Query on PRD_000383
B BOC-PHE-PSI[CH2CH2NH]-PHE-GLU-PHE-NH2 Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.178
  • Space Group: P 61
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 62.70 α = 90.00
b = 62.70 β = 90.00
c = 82.23 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-06-12
  • Released Date: 2004-01-13
  • Deposition author(s): Petrokova, H., Hasek, J., Dohnalek, J.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Source and taxonomy | Details: update source
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values