7E1J | pdb_00007e1j

Crystal structure of Pr55Gag-matrix domain in complex with IP6 in space group C121

• PDB DOI: https://doi.org/10.2210/pdb7E1J/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-02-01 Released: 2021-08-04 
• Deposition Author(s): DeMirci, H., Senda, T., Destan, E.
• Funding Organization(s): National Science Foundation (NSF, United States), Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 
  0.272 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of Pr55Gag-matrix domain in complex with IP6 in space group C121

DeMirci, H., Senda, T., Destan, E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 83.78 kDa 
• Atom Count: 5,706 
• Modeled Residue Count: 665 
• Deposited Residue Count: 702 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A, B, C, D, E, F	117	Human immunodeficiency virus 1	Mutation(s): 0  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free:  0.272 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.182	α = 90
b = 67.414	β = 123.15
c = 97.499	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): DeMirci, H., Senda, T., Destan, E.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	NSF-1231306
Other government	Turkey	118C270

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references