6EAK | pdb_00006eak

CRYSTAL STRUCTURE OF FUSION INHIBITOR JNJ-2408068 IN COMPLEX WITH HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN ESCAPE VARIANT T400A STABILIZED IN THE PREFUSION STATE

PDB DOI: https://doi.org/10.2210/pdb6EAK/pdb

Classification: VIRAL PROTEIN
Organism(s): human respiratory syncytial virus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2018-08-03 Released: 2019-08-07
Deposition Author(s): Battles, M.B., McLellan, J.S.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.221 (Depositor), 0.227 (DCC)
R-Value Work:
0.191 (Depositor), 0.197 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Basis for Respiratory Syncytial Virus Fusion Inhibitor Resistance

Battles, M.B., McLellan, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 64.43 kDa
Atom Count: 3,512
Modeled Residue Count: 438
Deposited Residue Count: 568
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A [auth F]	568	human respiratory syncytial virus	Mutation(s): 5
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420 Go to UniProtKB: P03420
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03420
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5NK (Subject of Investigation/LOI) Query on 5NK Download:Ideal Coordinates CCD File SDF format, chain J [auth F] MOL2 format, chain J [auth F] mmCIF format, chain J [auth F]	J [auth F]	2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol C₂₂ H₃₀ N₆ O RDQSNNMSDOHAPG-UHFFFAOYSA-N		Interactions Focus chain J [auth F] Interactions & Density Focus chain J [auth F]
NHE Query on NHE Download:Ideal Coordinates CCD File SDF format, chain H [auth F] MOL2 format, chain H [auth F] mmCIF format, chain H [auth F]	H [auth F]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain H [auth F] Interactions & Density Focus chain H [auth F]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth F] SDF format, chain C [auth F] SDF format, chain D [auth F] SDF format, chain E [auth F] SDF format, chain F SDF format, chain G [auth F] MOL2 format, chain B [auth F] MOL2 format, chain C [auth F] MOL2 format, chain D [auth F] MOL2 format, chain E [auth F] MOL2 format, chain F MOL2 format, chain G [auth F] mmCIF format, chain B [auth F] mmCIF format, chain C [auth F] mmCIF format, chain D [auth F] mmCIF format, chain E [auth F] mmCIF format, chain F mmCIF format, chain G [auth F]	B [auth F] C [auth F] D [auth F] E [auth F] F B [auth F], C [auth F], D [auth F], E [auth F], F, G [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth F] Focus chain C [auth F] Focus chain D [auth F] Focus chain E [auth F] Focus chain F Focus chain G [auth F] Interactions & Density Focus chain B [auth F] Focus chain C [auth F] Focus chain D [auth F] Focus chain E [auth F] Focus chain F Focus chain G [auth F]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain I [auth F] MOL2 format, chain I [auth F] mmCIF format, chain I [auth F]	I [auth F]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain I [auth F] Interactions & Density Focus chain I [auth F]

Binding Affinity Annotations
ID	Source	Binding Affinity
5NK	BindingDB: 6EAK	EC50: 0.16 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.221 (Depositor), 0.227 (DCC)
R-Value Work: 0.191 (Depositor), 0.197 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.45	α = 90
b = 168.45	β = 90
c = 168.45	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-08-07

Deposition Author(s):

Battles, M.B.

McLellan, J.S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5T32AI007519-18
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM113132

Revision History (Full details and data files)

Version 1.0: 2019-08-07
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-09
Changes: Structure summary