5TC2 | pdb_00005tc2

C-terminal domain of HIV-1 integrase, crystal structure

• PDB DOI: https://doi.org/10.2210/pdb5TC2/pdb

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2016-09-14 Released: 2018-04-04 
• Deposition Author(s): Tsirkone, V.G., Strelkov, S.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.240 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Interaction of TRN-SR2 with HIV Integrase

Tsirkone, V.G., Strelkov, S.V.

To be published.

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 (software)

Macromolecule Content 

• Total Structure Weight: 13.74 kDa 
• Atom Count: 1,006 
• Modeled Residue Count: 110 
• Deposited Residue Count: 112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
integrase	A, B	56	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: pol
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.240 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.139	α = 90
b = 72.618	β = 106.39
c = 33.893	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-04 
Deposition Author(s): Tsirkone, V.G., Strelkov, S.V.

Revision History  

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description