9EE2 | pdb_00009ee2

HIV CA - FSFG peptide (14 mM)

PDB DOI: https://doi.org/10.2210/pdb9EE2/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free:
0.253 (Depositor), 0.253 (DCC)
R-Value Work:
0.233 (Depositor), 0.233 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Structure of HIV capsid protein with FSFG peptide (14 mM)

Melcak, I.

To be published.

Macromolecule Content

Total Structure Weight: 315.82 kDa
Atom Count: 19,425
Modeled Residue Count: 2,560
Deposited Residue Count: 2,871
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A, B, C, D, E 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12493
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain X [auth E] MOL2 format, chain X [auth E] mmCIF format, chain X [auth E]	X [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain X [auth E] Interactions & Density Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free: 0.253 (Depositor), 0.253 (DCC)
R-Value Work: 0.233 (Depositor), 0.233 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.408	α = 90
b = 136.447	β = 90
c = 208.854	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-18

Deposition Author(s):

Sarafianos, S.G.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.