9EDZ | pdb_00009edz

HIV CA - GLFG peptide (4 mM)

• PDB DOI: https://doi.org/10.2210/pdb9EDZ/pdb

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


• Deposited: 2024-11-18 Released: 2026-03-18 
• Deposition Author(s): Melcak, I., Sarafianos, S.G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.267 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Structure of HIV capsid protein with GLFG peptide (4 mM)

Melcak, I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A6B1C1D1 Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A6B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B1C1D1 

Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 315.08 kDa 
• Atom Count: 19,212 
• Modeled Residue Count: 2,558 
• Deposited Residue Count: 2,871 
• Unique protein chains: 2

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	231	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 4  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLFG peptide	M [auth N], N [auth O], O [auth P], P [auth R], Q [auth S], R [auth V], S [auth W], T [auth M], U [auth Q], V [auth U], W [auth X]	9	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.267 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.547	α = 90
b = 136.778	β = 90
c = 208.195	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-18 
Deposition Author(s): Melcak, I., Sarafianos, S.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI176946

Revision History  

• Version 1.0: 2026-03-18
  Type: Initial release