8F22 | pdb_00008f22

HIV-CA Disulfide linked Hexamer bound to 11l capsid inhibitor.

• PDB DOI: https://doi.org/10.2210/pdb8F22/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-11-06 Released: 2023-09-13 
• Deposition Author(s): Barnett, M.J., Goldstone, D.C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.347 (Depositor), 0.350 (DCC) 
• R-Value Work: 
  0.310 (Depositor), 0.310 (DCC) 
• R-Value Observed: 
  0.312 (Depositor) 

Starting Model: experimental

Literature

Structure of a benzosulfonamide based inhibitor - bound to a disulfide stabilised HIV-1 capsid hexamer

Barnett, M., Sun, L., Xu, S., Liu, X., Zhan, P., Goldstone, D.C.

(2023) bioRxiv 

• DOI: https://doi.org/10.1101/2023.08.16.553511

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 299.83 kDa 
• Atom Count: 17,342 
• Modeled Residue Count: 2,234 
• Deposited Residue Count: 2,688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A, B, C, D, E, F, G, H, I, J, K, L	224	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 4  Gene Names: gag-pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XBQ (Subject of Investigation/LOI)	M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F]	Nalpha-{[4-(4-aminobenzene-1-sulfonyl)-2-oxopiperazin-1-yl]acetyl}-N-(4-methoxyphenyl)-N-methyl-L-phenylalaninamide C29 H33 N5 O6 S REXBCEZWZOLFMN-SANMLTNESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.347 (Depositor), 0.350 (DCC) 
• R-Value Work:  0.310 (Depositor), 0.310 (DCC) 
• R-Value Observed: 0.312 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.951	α = 87.17
b = 91.186	β = 78.77
c = 116.266	γ = 60.37

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Barnett, M.J., Goldstone, D.C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary