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 
- Funding Organization(s): UK
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 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Envelope glycoprotein,GP,GP1 | 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 Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q05320 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Envelope glycoprotein | 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... | ||
UniProt | |||||
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q05320 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
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 | 3D Interactions | |
8PR Query on 8PR | L [auth A] | Paroxetine C19 H20 F N O3 AHOUBRCZNHFOSL-YOEHRIQHSA-N | |||
NAG Query on 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 Query on GOL | I [auth A], J [auth A], K [auth A], M [auth B], N [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
DMS Query on DMS | H [auth A] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |
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 Name | Purpose |
---|---|
PHENIX | refinement |
xia2 | data reduction |
xia2 | data scaling |
REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-01-03  Deposition Author(s): Ren, J., Zhao, Y., Fry, E.E., Stuart, D.I.
Funding Organization | Location | Grant Number |
---|---|---|
UK | United Kingdom | MR/N00065X/1 |
Revision History (Full details and data files)
- 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