6F6I

CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH PAROXETINE

• PDB DOI: https://doi.org/10.2210/pdb6F6I/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Ebola virus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2017-12-05 Released: 2018-01-03 
• Deposition Author(s): Ren, J., Zhao, Y., Fry, E.E., Stuart, D.I.
• Funding Organization(s): UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.212 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 57.73 kDa 
• Atom Count: 3,320 
• Modelled Residue Count: 382 
• Deposited Residue Count: 498 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein,GP,GP1	A	330	Ebola virus	Mutation(s): 1  Gene Names: GP, DH33_45402gpGP
UniProt
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein	B	168	Ebola virus	Mutation(s): 1  Gene Names:  GP, DF49_53415gpGP, DF49_53416gpGP, DF49_53417gpGP, DF49_53418gpGP, DF49_53419gpGP, DF49_53420gpGP, DF49_53421gpGP, DF49_53422gpGP, DF49_53423gpGP, DF49_53424gpGP, DF49_53425gpGP, DF49_53426gpGP
UniProt
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8PR	L [auth A]	Paroxetine C19 H20 F N O3 AHOUBRCZNHFOSL-YOEHRIQHSA-N
NAG	D [auth A], E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	I [auth A], J [auth A], K [auth A], M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8PR	Binding MOAD:  6F6I	Kd: 6.50e+5 (nM) from 1 assay(s)
	BindingDB:  6F6I	Kd: 6.50e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.212 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.68	α = 90
b = 113.68	β = 90
c = 306.26	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-01-03 
Deposition Author(s): Ren, J., Zhao, Y., Fry, E.E., Stuart, D.I.

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Funding Organization	Location	Grant Number
UK	United Kingdom	MR/N00065X/1

Revision History  

• Version 1.0: 2018-01-03
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2018-02-21
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary