Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0074953
Abendroth, J., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.To be published.
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
Starting Model: experimental
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This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Molecule | Chains | Sequence Length | Organism | Details | Image |
|---|---|---|---|---|---|
| GP1 | 290 | Ebola virus - Mayinga, Zaire, 1976 | Mutation(s): 1 Gene Names: GP | ||
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320 Go to UniProtKB: Q05320 | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q05320 | ||||
| Glycosylation Sites: 4 | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Molecule | Chains | Sequence Length | Organism | Details | Image |
|---|---|---|---|---|---|
| GP2 | 168 | Ebola virus - Mayinga, Zaire, 1976 | Mutation(s): 1 Gene Names: GP | ||
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320 Go to UniProtKB: Q05320 | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q05320 | ||||
| Glycosylation Sites: 1 | |||||
| |||||
Oligosaccharides
| 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 | ||
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 - Version 1.2: 2024-11-06
Changes: Structure summary