5YT9 | pdb_00005yt9

Crystal structure of H5 hemagglutinin G228S mutant from A/chicken/Taiwan/0502/2012

PDB DOI: https://doi.org/10.2210/pdb5YT9/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/chicken/Taiwan/0502/2012(H5N2))
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2017-11-17 Released: 2018-11-21
Deposition Author(s): Lin, T.H., Lee, M.S., Wu, W.G., Liu, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free:
0.272 (Depositor), 0.273 (DCC)
R-Value Work:
0.215 (Depositor), 0.215 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

crystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012

Lin, T.H., Lee, M.S., Wu, W.G., Liu, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 66.58 kDa
Atom Count: 3,990
Modeled Residue Count: 495
Deposited Residue Count: 586
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	586	Influenza A virus (A/chicken/Taiwan/0502/2012(H5N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A059VBQ9 (Influenza A virus) Explore A0A059VBQ9 Go to UniProtKB: A0A059VBQ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A059VBQ9
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.272 (Depositor), 0.273 (DCC)
R-Value Work: 0.215 (Depositor), 0.215 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.81	α = 90
b = 111.81	β = 90
c = 313.596	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Funding Organization	Location	Grant Number
	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-10-23
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.