6R8C | pdb_00006r8c

HIV capsid hexamer with IP5 ligand

• PDB DOI: https://doi.org/10.2210/pdb6R8C/pdb

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


• Deposited: 2019-04-01 Released: 2020-05-06 
• Deposition Author(s): James, L.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

HIV hexamer

James, L.C.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 23.55 kDa 
• Atom Count: 1,840 
• Modeled Residue Count: 205 
• Deposited Residue Count: 205 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag polyprotein	A	205	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag
UniProt
Find proteins for B6DRA0 (Human immunodeficiency virus type 1) Explore B6DRA0  Go to UniProtKB:  B6DRA0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5MY (Subject of Investigation/LOI)	B [auth A]	MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE C6 H17 O21 P5 CTPQAXVNYGZUAJ-KXXVROSKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.663	α = 90
b = 90.663	β = 90
c = 56.997	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): James, L.C.

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary