5VMJ
Influenza hemagglutinin H1 mutant DH1E in complex with 3'SLN
- PDB DOI: https://doi.org/10.2210/pdb5VMJ/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Influenza A virus (A/New_York/1/18(H1N1)), Influenza A virus (A/Brevig Mission/1/1918(H1N1))
- Expression System: unidentified baculovirus
- Mutation(s): Yes
- Deposited: 2017-04-27 Released: 2017-11-08
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.95 Å
- R-Value Free: 0.248
- R-Value Work: 0.208
- R-Value Observed: 0.210
This is version 2.2 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 HA1 | 326 | Influenza A virus (A/New_York/1/18(H1N1)) | Mutation(s): 3 Gene Names: HA |  | |
UniProt | |||||
Find proteins for Q9WFX4 (Influenza A virus) Explore Q9WFX4 Go to UniProtKB: Q9WFX4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9WFX4 | ||||
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 HA2 | 191 | Influenza A virus (A/Brevig Mission/1/1918(H1N1)) | Mutation(s): 0 Gene Names: HA |  | |
UniProt | |||||
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9WFX3 Go to UniProtKB: Q9WFX3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9WFX3 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose | G, I, J | 2 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G30207PZ GlyCosmos: G30207PZ GlyGen: G30207PZ | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | L [auth A], M [auth C], N [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.95 Å
- R-Value Free: 0.248
- R-Value Work: 0.208
- R-Value Observed: 0.210
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 95.94 | α = 90 |
| b = 81.05 | β = 91.13 |
| c = 120.95 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-11-08 Deposition Author(s): Ni, F., Kondrashkina, E., Wang, Q.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R01-AI067839 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01-GM116280) |
Revision History (Full details and data files)
- Version 1.0: 2017-11-08
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2022-03-23
Changes: Author supporting evidence, Database references, Derived calculations, Structure summary - Version 2.2: 2023-10-04
Changes: Data collection, Refinement description
