5LBV
Structural basis of zika and dengue virus potent antibody cross-neutralization
- PDB DOI: https://doi.org/10.2210/pdb5LBV/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Zika virus
- Expression System: Drosophila melanogaster
- Mutation(s): No
- Membrane Protein: Yes OPM
- Deposited: 2016-06-17 Released: 2016-07-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.239
- R-Value Work: 0.207
- R-Value Observed: 0.209
wwPDB Validation 3D Report Full Report
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 protein E | 447 | Zika virus | Mutation(s): 0 Membrane Entity: Yes |  | |
UniProt | |||||
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1 Go to UniProtKB: A0A024B7W1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A024B7W1 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | C | 5 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42466VF GlyCosmos: G42466VF GlyGen: G42466VF | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NA Query on NA | D [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.239
- R-Value Work: 0.207
- R-Value Observed: 0.209
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 64.628 | α = 90 |
| b = 213.566 | β = 90 |
| c = 124.024 | γ = 90 |
| Software Name | Purpose |
|---|---|
| BUSTER | refinement |
| XDS | data reduction |
| Aimless | data scaling |
Entry History
Deposition Data
- Released Date: 2016-07-06 Deposition Author(s): Barba-Spaeth, G.
Revision History (Full details and data files)
- Version 1.0: 2016-07-06
Type: Initial release - Version 1.1: 2016-07-20
Changes: Database references - Version 1.2: 2016-08-17
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: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
