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), 0.243 (DCC)
R-Value Work:
0.191 (Depositor), 0.203 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6R8C

Ligand Structure Quality Assessment

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: 23.55 kDa
Atom Count: 1,840
Modeled Residue Count: 205
Deposited Residue Count: 205
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B6DRA0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5MY (Subject of Investigation/LOI) Query on 5MY Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE C₆ H₁₇ O₂₁ P₅ CTPQAXVNYGZUAJ-KXXVROSKSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.234 (Depositor), 0.243 (DCC)
R-Value Work: 0.191 (Depositor), 0.203 (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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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: 2024-10-23
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.