7M2D
Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0074953
- PDB DOI: https://doi.org/10.2210/pdb7M2D/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Ebola virus - Mayinga, Zaire, 1976
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2021-03-16 Released: 2021-11-24 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.225 
- R-Value Work: 0.189 
- R-Value Observed: 0.192 
This is version 1.1 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 |
GP1 | 290 | Ebola virus - Mayinga, Zaire, 1976 | 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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
GP2 | 168 | Ebola virus - Mayinga, Zaire, 1976 | 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 AnnotationsExpand | |||||
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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 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
YPS Query on YPS | H [auth A] | (1R,3S,5R,7R)-N-[(1r,4R)-4-aminocyclohexyl]-3-(ethoxymethyl)-5-phenyladamantane-1-carboxamide C26 H38 N2 O2 QUVAMRWCRBWKIJ-OKWRYAMFSA-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 |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.225 
- R-Value Work: 0.189 
- R-Value Observed: 0.192 
- Space Group: H 3 2
- Diffraction Data: https://doi.org/10.18430/M37M2D
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 115.11 | α = 90 |
b = 115.11 | β = 90 |
c = 309.02 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |
PHENIX | model building |
Coot | model building |
Entry History 
Deposition Data
- Released Date: 2021-11-24  Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2021-11-24
Type: Initial release - Version 1.1: 2023-10-18
Changes: Data collection, Refinement description