6EX9 | pdb_00006ex9

Crystal Structure of HIV-1 Integrase Catalytic Core Domain with Inhibitor Peptide

• PDB DOI: https://doi.org/10.2210/pdb6EX9/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-11-07 Released: 2018-06-06 
• Deposition Author(s): Galilee, M., Alian, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.279 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Multimerization of HIV-1 integrase hinges on conserved SH3-docking platforms

Galilee, M., Alian, A.

(2018) bioRxiv 

• DOI: https://doi.org/10.1101/301721

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.56 kDa 
• Atom Count: 1,228 
• Modeled Residue Count: 155 
• Deposited Residue Count: 167 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A	152	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inhibitor Peptide	B	15	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.279 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.519	α = 90
b = 96.519	β = 90
c = 48.489	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-06 
Deposition Author(s): Galilee, M., Alian, A.

Revision History  

• Version 1.0: 2018-06-06
  Type: Initial release
  
• Version 1.1: 2019-08-21
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description