3BVA

Cystal structure of HIV-1 Active Site Mutant D25N and p2-NC analog inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.150

Literature

Macromolecules
Sequence Display for 3BVA

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 22526.65

Macromolecule Entities
Molecule Chains Length Organism Details
Protease (Retropepsin) A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Mutation: Q7K, D25N, L33I, L63I, C67A, C95A
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
2NC
Query on 2NC

B N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}- L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]- L-ornithinamide
p2/NC (Synonym)
C35 H68 N11 O8
MQPXOVRKKPPKFZ-QYKDHROSSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, 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 %)
2NC N/A in BindingDB
Ka: 31.7 M-1  BindingMOAD
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000398
Query on PRD_000398
B N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) 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: 1.05 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.150
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 58.20 α = 90.00
b = 85.89 β = 90.00
c = 46.55 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-01-05
  • Released Date: 2008-04-01
  • Deposition author(s): Liu, F., Weber, I.T.

Revision History

  • Version 1_0: 2008-04-01

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance

  • Version 1_2: 2013-02-27

    Type: Other