5VLI
Computationally designed inhibitor peptide HB1.6928.2.3 in complex with influenza hemagglutinin (A/PuertoRico/8/1934)
- PDB DOI: https://doi.org/10.2210/pdb5VLI/pdb
- Classification: VIRAL PROTEIN/DE NOVO PROTEIN
- Organism(s): Influenza A virus (A/Puerto Rico/8/1934(H1N1)), synthetic construct
- Expression System: Trichoplusia ni
- Mutation(s): No 
- Deposited: 2017-04-25 Released: 2017-09-27 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.213 
- R-Value Work: 0.182 
- R-Value Observed: 0.183 
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 |
Hemagglutinin | 327 | Influenza A virus (A/Puerto Rico/8/1934(H1N1)) | Mutation(s): 0  Gene Names: HA | ||
UniProt | |||||
Find proteins for P03452 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)) Explore P03452  Go to UniProtKB:  P03452 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P03452 | ||||
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 |
Hemagglutinin | 176 | Influenza A virus (A/Puerto Rico/8/1934(H1N1)) | Mutation(s): 0  Gene Names: HA | ||
UniProt | |||||
Find proteins for P03452 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)) Explore P03452  Go to UniProtKB:  P03452 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P03452 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Computationally designed peptide HB1.6928.2.3 | 40 | synthetic construct | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | F [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
PGF Query on PGF | G [auth A] | 2,5,8,11-TETRAOXATRIDECANE C9 H20 O4 JRRDISHSXWGFRF-UHFFFAOYSA-N | |||
PEG Query on PEG | H [auth B], I [auth B], J [auth C] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.213 
- R-Value Work: 0.182 
- R-Value Observed: 0.183 
- Space Group: H 3 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 110.649 | α = 90 |
b = 110.649 | β = 90 |
c = 327.378 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-09-27  Deposition Author(s): Bernard, S.M., Wilson, I.A.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R56AI117675 |
Revision History (Full details and data files)
- Version 1.0: 2017-09-27
Type: Initial release - Version 1.1: 2017-10-11
Changes: Database references - Version 1.2: 2017-10-18
Changes: Database references - Version 1.3: 2019-12-11
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary