2A1E

High resolution structure of HIV-1 PR with TS-126

• PDB DOI: https://doi.org/10.2210/pdb2A1E/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-06-20 Released: 2006-02-21 
• Deposition Author(s): Demitri, N., Geremia, S., Randaccio, L., Wuerges, J., Benedetti, F., Berti, F., Dinon, F., Campaner, P., Tell, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.201 
• R-Value Work: 0.156 
• R-Value Observed: 0.156 

Starting Model: experimental

Literature

A potent HIV protease inhibitor identified in an epimeric mixture by high-resolution protein crystallography.

Geremia, S., Demitri, N., Wuerges, J., Benedetti, F., Berti, F., Tell, G., Randaccio, L.

(2006) ChemMedChem 1: 186-188

• PubMed: 16892350 
• DOI: https://doi.org/10.1002/cmdc.200500063
• Primary Citation of Related Structures:  
  2A1E

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Organizational Affiliation: 

Department of Chemical Sciences and Centre of Excellence in Biocrystallography, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 23.05 kDa 
• Atom Count: 1,917 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pol polyprotein	A, B	99	Human immunodeficiency virus 1	Mutation(s): 5  Gene Names: GAG-POL EC: 3.4.23.16
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPF	K [auth B]	N-ACETYLTRYPTOPHYL-N~1~-{3-[1-(N-ACETYLTRYPTOPHYLVALYL)PYRROLIDIN-2-YL]-1-BENZYL-2,3-DIHYDROXYPROPYL}VALINAMIDE C50 H64 N8 O8 BDIYLIYACVEIHS-QVWIHFFISA-N
GOL	M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	C [auth A], D [auth A], E [auth A], F [auth A], L [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT	I [auth B], J [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.201 
• R-Value Work: 0.156 
• R-Value Observed: 0.156 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.269	α = 90
b = 84.956	β = 90
c = 46.061	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
SHELXL-97	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-21 
Deposition Author(s): Demitri, N., Geremia, S., Randaccio, L., Wuerges, J., Benedetti, F., Berti, F., Dinon, F., Campaner, P., Tell, G.

Revision History  

• Version 1.0: 2006-02-21
  Type: Initial release
  
• Version 1.1: 2007-10-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2023-10-25
  Changes: Data collection, Refinement description