6ERN | pdb_00006ern

HIV Hexamer with ligand

PDB DOI: https://doi.org/10.2210/pdb6ERN/pdb

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

Deposited: 2017-10-18 Released: 2018-11-07
Deposition Author(s): James, L.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.237 (Depositor), 0.244 (DCC)
R-Value Work:
0.185 (Depositor), 0.199 (DCC)
R-Value Observed:
0.187 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

HIV hexamer

James, L.C.

To be published.

Macromolecule Content

Total Structure Weight: 24.71 kDa
Atom Count: 1,675
Modeled Residue Count: 202
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag polyprotein	A	216	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
ATP Query on ATP 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]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.237 (Depositor), 0.244 (DCC)
R-Value Work: 0.185 (Depositor), 0.199 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.846	α = 90
b = 90.846	β = 90
c = 56.747	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-11-07
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2020-04-01
Changes: Advisory, Derived calculations
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, 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.