4DVL
Crystal structure of the glycoprotein Erns from the pestivirus BVDV-1 in complex with 2'-3'-cyclo-UMP
- PDB DOI: https://doi.org/10.2210/pdb4DVL/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Bovine viral diarrhea virus 1-CP7
- Expression System: Drosophila melanogaster
- Mutation(s): No 
- Deposited: 2012-02-23 Released: 2012-05-23 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.249 
- R-Value Work: 0.197 
- R-Value Observed: 0.202 
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 |
E(rns) glycoprotein | 167 | Bovine viral diarrhea virus 1-CP7 | Mutation(s): 0  Gene Names: Erns | ||
UniProt | |||||
Find proteins for Q96662 (Bovine viral diarrhea virus (strain CP7)) Explore Q96662  Go to UniProtKB:  Q96662 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q96662 | ||||
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-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G51945PF GlyCosmos:  G51945PF GlyGen:  G51945PF |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO |
Entity ID: 4 | |||||
---|---|---|---|---|---|
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)-2-acetamido-2-deoxy-beta-D-glucopyranose | E | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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 | F | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G78727VW GlyCosmos:  G78727VW GlyGen:  G78727VW |
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
JKM Query on JKM | L [auth A], R [auth B] | 1-[(2S,3aS,4S,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4(
1H,3H)-dione C9 H11 N2 O8 P HWDMHJDYMFRXOX-GVYWOMJSSA-N | |||
NAG Query on NAG | H [auth A], I [auth A], M [auth B], N [auth B], O [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | J [auth A], K [auth A], P [auth B], Q [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.249 
- R-Value Work: 0.197 
- R-Value Observed: 0.202 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 70.515 | α = 90 |
b = 105.934 | β = 90 |
c = 63.405 | γ = 90 |
Software Name | Purpose |
---|---|
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data scaling |
XDS | data reduction |
BUSTER | refinement |
Entry History 
Deposition Data
- Released Date: 2012-05-23  Deposition Author(s): Krey, T., Bontems, F., Vonrhein, C., Vaney, M.-C., Bricogne, G., Ruemenapf, T., Rey, F.A.
Revision History (Full details and data files)
- Version 1.0: 2012-05-23
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary