6EAI

CRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN INHIBITOR ESCAPE VARIANT S398L STABILIZED IN THE PREFUSION STATE

PDB DOI: https://doi.org/10.2210/pdb6EAI/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: 2.80 Å
R-Value Free: 0.239
R-Value Work: 0.210
R-Value Observed: 0.211

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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: 193 kDa
Atom Count: 10,249
Modelled Residue Count: 1,293
Deposited Residue Count: 1,704
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, B, C	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03420
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain R [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain R [auth C] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain R [auth C]	D [auth A], J [auth B], R [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain R [auth C]
NHE Query on NHE Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	H [auth A] I [auth A] O [auth B] P [auth B] W [auth C] H [auth A], I [auth A], O [auth B], P [auth B], W [auth C], X [auth C]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain W [auth C] Focus chain X [auth C]
TAR Query on TAR Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain Y [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth C]	Q [auth B], Y [auth C]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain Q [auth B] Focus chain Y [auth C] Interactions & Density Focus chain Q [auth B] Focus chain Y [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	E [auth A] F [auth A] G [auth A] K [auth B] L [auth B] E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], M [auth B], N [auth B], S [auth C], T [auth C], U [auth C], V [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.239
R-Value Work: 0.210
R-Value Observed: 0.211
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.319	α = 90
b = 167.319	β = 90
c = 174.43	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary