6VMZ
Crystal Structure of a H5N1 influenza virus hemagglutinin with CBS1117
- PDB DOI: https://doi.org/10.2210/pdb6VMZ/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Influenza A virus (A/chicken/Vietnam/4/2003(H5N1)), Influenza A virus (A/chicken/Vietnam/30/2003(H5N1))
- Expression System: Trichoplusia ni
- Mutation(s): No
- Deposited: 2020-01-28 Released: 2020-07-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.252
- R-Value Work: 0.208
- R-Value Observed: 0.210
wwPDB Validation 3D Report Full Report
Currently 6VMZ does not have a validation slider image.
This is version 1.3 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 | A, B [auth C], C [auth E] | 334 | Influenza A virus (A/chicken/Vietnam/4/2003(H5N1)) | Mutation(s): 0 Gene Names: HA |  |
UniProt | |||||
Find proteins for Q1KHJ8 (Influenza A virus) Explore Q1KHJ8 Go to UniProtKB: Q1KHJ8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q1KHJ8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Hemagglutinin | D [auth B], E [auth D], F | 181 | Influenza A virus (A/chicken/Vietnam/30/2003(H5N1)) | Mutation(s): 0 Gene Names: HA |  |
UniProt | |||||
Find proteins for Q1KHK7 (Influenza A virus) Explore Q1KHK7 Go to UniProtKB: Q1KHK7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q1KHK7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| R3P (Subject of Investigation/LOI) Query on R3P | J [auth A], N [auth C], Q [auth E] | 2,6-dichloro-N-[1-(propan-2-yl)piperidin-4-yl]benzamide C15 H20 Cl2 N2 O OUZZSIOQTSNTTI-UHFFFAOYSA-N |  | ||
| NAG Query on NAG | G [auth A] H [auth A] I [auth A] K [auth C] L [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: 2.20 Å
- R-Value Free: 0.252
- R-Value Work: 0.208
- R-Value Observed: 0.210
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.71 | α = 90 |
| b = 126.083 | β = 90 |
| c = 249.639 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
| PDB_EXTRACT | data extraction |
Structure Validation
Currently 6VMZ does not have a validation slider image.
Entry History
Deposition Data
- Released Date: 2020-07-01 Deposition Author(s): Antanasijevic, A., Durst, M.A., Lavie, A., Caffrey, M.
Revision History (Full details and data files)
- Version 1.0: 2020-07-01
Type: Initial release - Version 1.1: 2020-07-15
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary
