6AXV | pdb_00006axv

Structure of the T58S/T107I/P122A mutant of the HIV-1 capsid protein in complex with PF-3450074 (PF74)

• PDB DOI: https://doi.org/10.2210/pdb6AXV/pdb

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


• Deposited: 2017-09-07 Released: 2018-09-12 
• Deposition Author(s): Gres, A.T., Kirby, K.A., Sarafianos, S.G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 
  0.279 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Identification of a novel element in HIV-1 capsid critical for assembly and maturation

Novikova, M., Gres, A.T., Kirby, K.A., Sarafianos, S.G., Freed, E.O.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 26.98 kDa 
• Atom Count: 1,743 
• Modeled Residue Count: 215 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 capsid protein	A	231	Human immunodeficiency virus 1	Mutation(s): 3  Gene Names: Gag
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12493  Go to UniProtKB:  P12493

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1B0	P [auth A]	N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE C27 H27 N3 O2 ACDFWSNAQWFRRF-VWLOTQADSA-N
IOD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free:  0.279 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.998	α = 90
b = 92.998	β = 90
c = 57.631	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
Blu-Ice	data collection
PHENIX	refinement
PDB_EXTRACT	data extraction
Aimless	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Gres, A.T., Kirby, K.A., Sarafianos, S.G.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI120860

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary