Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22976.96 
• Atom Count: 1629 
• Residue Count: 208 
• Unique protein chains: 2

2FNS

Crystal structure of wild-type inactive (D25N) HIV-1 protease complexed with wild-type HIV-1 NC-p1 substrate.

• DOI: 10.2210/pdb2FNS/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2006-01-11 Released: 2006-09-05 
• Deposition Author(s): Prabu-Jeyabalan, M., Nalivaika, E.A., Schiffer, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.243 
• R-Value Work: 0.195 

Literature

Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate.

Prabu-Jeyabalan, M., Nalivaika, E.A., Romano, K., Schiffer, C.A.

(2006) J.Virol. 80: 3607-3616

• PubMed: 16537628 
• DOI: 10.1128/JVI.80.7.3607-3616.2006
• Primary Citation of Related Structures:  
  2FNT


• PubMed Abstract: 
  

Human immunodeficiency virus type 1 (HIV-1) protease processes and cleaves the Gag and Gag-Pol polyproteins, allowing viral maturation, and therefore is an important target for antiviral therapy. Ligand binding occurs when the flaps open, allowing access to the active site. This flexibility in flap geometry makes trapping and crystallizing structural intermediates in substrate binding challenging. In this study, we report two crystal structures of two HIV-1 protease variants bound with their corresponding nucleocapsid-p1 variant. One of the flaps in each of these structures exhibits an unusual "intermediate" conformation. Analysis of the flap-intermediate and flap-closed crystal structures reveals that the intermonomer flap movements may be asynchronous and that the flap which wraps over the P3 to P1 (P3-P1) residues of the substrate might close first. This is consistent with our hypothesis that the P3-P1 region is crucial for substrate recognition. The intermediate conformation is conserved in both the wild-type and drug-resistant variants. The structural differences between the variants are evident only when the flaps are closed. Thus, a plausible structural model for the adaptability of HIV-1 protease to recognize substrates in the presence of drug-resistant mutations has been proposed.

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Related Citations: 

• Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease.
  Prabu-Jeyabalan, M.,Nalivaika, E.A.,King, N.M.,Schiffer, C.A.
  (2004) J.Virol. 78: 12446




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Organizational Affiliation: 

Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Protease	A, B	99	Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)	Mutation(s): 3  Gene Names: gag-pol
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)) Go to UniProtKB:  P03369

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
NC-P1 SUBSTRATE PEPTIDE	P	10	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	B	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	A, B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.243 
• R-Value Work: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 51.060	α = 90.00
b = 57.369	β = 90.00
c = 61.302	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-11 
• Released Date: 2006-09-05 
• Deposition Author(s): Prabu-Jeyabalan, M., Nalivaika, E.A., Schiffer, C.A.

Revision History 

• Version 1.0: 2006-09-05
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-18
  Type: Refinement description