1SP5 | pdb_00001sp5

Crystal structure of HIV-1 protease complexed with a product of autoproteolysis

• PDB DOI: https://doi.org/10.2210/pdb1SP5/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-03-16 Released: 2005-07-19 
• Deposition Author(s): Vondrackova, E., Hasek, J., Jaskolski, M., Rezacova, P., Dohnalek, J., Skalova, T., Petrokova, H., Duskova, J., Brynda, J., Sedlacek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.211 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Product of enzymatic self-cleavage bound in the active site of HIV protease

Vondrackova, E., Hasek, J., Jaskolski, M., Rezacova, P., Dohnalek, J., Skalova, T., Petrokova, H., Duskova, J., Brynda, J., Sedlacek, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Macromolecule Content 

• Total Structure Weight: 22.68 kDa 
• Atom Count: 1,721 
• Modeled Residue Count: 203 
• Deposited Residue Count: 203 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5-mer peptide from Protease	C [auth I]	5	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: POL
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	F [auth A], G [auth A], J [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
DMS	H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	D [auth A], E [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.211 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.765	α = 90
b = 86.284	β = 90
c = 45.834	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-19 
Deposition Author(s): Vondrackova, E., Hasek, J., Jaskolski, M., Rezacova, P., Dohnalek, J., Skalova, T., Petrokova, H., Duskova, J., Brynda, J., Sedlacek, J.

Revision History  

• Version 1.0: 2005-07-19
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description