6F6S

CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH benztropine

PDB DOI: https://doi.org/10.2210/pdb6F6S/pdb

Classification: VIRAL PROTEIN
Organism(s): Ebola virus - Mayinga, Zaire, 1976, Ebola virus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2017-12-06 Released: 2018-01-03
Deposition Author(s): Ren, J., Zhao, Y., Fry, E.E., Stuart, D.I.
Funding Organization(s): UK

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.233
R-Value Work: 0.207
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 58.34 kDa
Atom Count: 3,245
Modelled Residue Count: 379
Deposited Residue Count: 497
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein,Envelope glycoprotein,GP1	A	329	Ebola virus - Mayinga, Zaire, 1976, Ebola virus	Mutation(s): 1 Gene Names: GP
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 Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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... 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05320
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CXQ Query on CXQ Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain U [auth B] MOL2 format, chain I [auth A] MOL2 format, chain U [auth B]	I [auth A], U [auth B]	benztropine C₂₁ H₂₅ N O GIJXKZJWITVLHI-PMOLBWCYSA-N		Interactions Focus chain I [auth A] Focus chain U [auth B] Interactions & Density Focus chain I [auth A] Focus chain U [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth B]	C [auth A], D [auth A], E [auth A], F [auth A], Q [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain Q [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	G [auth A], H [auth A], R [auth B], S [auth B], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] J [auth A] K [auth A] L [auth A] M [auth A] AA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
CXQ	Binding MOAD: 6F6S	Kd: 1.30e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.233
R-Value Work: 0.207
R-Value Observed: 0.208
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.379	α = 90
b = 114.379	β = 90
c = 305.749	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-01-03

Deposition Author(s):

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 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary