6R6Q | pdb_00006r6q

HIV capsid hexamer with IP5 ligand

PDB DOI: https://doi.org/10.2210/pdb6R6Q/pdb

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

Deposited: 2019-03-27 Released: 2020-05-06
Deposition Author(s): James, L.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free:
0.289 (Depositor), 0.286 (DCC)
R-Value Work:
0.221 (Depositor), 0.226 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

HIV hexamer

James, L.C.

To be published.

Macromolecule Content

Total Structure Weight: 24.5 kDa
Atom Count: 1,612
Modeled Residue Count: 205
Deposited Residue Count: 219
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag polyprotein	A	219	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12493
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free: 0.289 (Depositor), 0.286 (DCC)
R-Value Work: 0.221 (Depositor), 0.226 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.693	α = 90
b = 90.693	β = 90
c = 56.958	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-05-06

Deposition Author(s):

Revision History (Full details and data files)

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: 2024-11-06
Changes: Structure summary

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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.