3BVA

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

Structural Biology Knowledgebase: 3BVA SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3BVA

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 22526.87

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

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
 
JSmol
GOL
Query on GOL

A, B GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
2NC Ki: 776 - 780 nM (92) BindingDB

Ka: 31.7 M-1  BindingMOAD
N/A in PDBbind

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
  • Electron Density Server: EDS EDS

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

  • 2013-02-27
    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: 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: Version format compliance | Details: compliance with PDB Exchange Dictionary V4