4WSX

The crystal structure of hemagglutinin from A/Jiangxi-Donghu/346/2013 influenza virus

PDB DOI: https://doi.org/10.2210/pdb4WSX/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2014-10-28 Released: 2015-02-25
Deposition Author(s): Yang, H., Carney, P.J., Chang, J.C., Villanueva, J.M., Stevens, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.266
R-Value Work: 0.243
R-Value Observed: 0.244

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 674.04 kDa
Atom Count: 46,260
Modelled Residue Count: 5,892
Deposited Residue Count: 6,012
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	327	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for A0A0J9X252 (Influenza A virus) Explore A0A0J9X252 Go to UniProtKB: A0A0J9X252
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0J9X252
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	174	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for A0A0J9X253 (Influenza A virus) Explore A0A0J9X253 Go to UniProtKB: A0A0J9X253
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0J9X253
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 AA [auth C] SDF format, chain BA [auth D] SDF format, chain CA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth G] SDF format, chain FA [auth H] SDF format, chain GA [auth I] SDF format, chain HA [auth J] SDF format, chain IA [auth K] SDF format, chain JA [auth L] SDF format, chain KA [auth M] SDF format, chain LA [auth N] SDF format, chain MA [auth O] SDF format, chain NA [auth P] SDF format, chain OA [auth Q] SDF format, chain PA [auth R] SDF format, chain QA [auth S] SDF format, chain RA [auth T] SDF format, chain SA [auth U] SDF format, chain UA [auth W] SDF format, chain VA [auth X] SDF format, chain Y [auth A] SDF format, chain Z [auth B] SDF format, chain TA [auth V] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth J] MOL2 format, chain IA [auth K] MOL2 format, chain JA [auth L] MOL2 format, chain KA [auth M] MOL2 format, chain LA [auth N] MOL2 format, chain MA [auth O] MOL2 format, chain NA [auth P] MOL2 format, chain OA [auth Q] MOL2 format, chain PA [auth R] MOL2 format, chain QA [auth S] MOL2 format, chain RA [auth T] MOL2 format, chain SA [auth U] MOL2 format, chain UA [auth W] MOL2 format, chain VA [auth X] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain TA [auth V]	AA [auth C] BA [auth D] CA [auth E] DA [auth F] EA [auth G] AA [auth C], BA [auth D], CA [auth E], DA [auth F], EA [auth G], FA [auth H], GA [auth I], HA [auth J], IA [auth K], JA [auth L], KA [auth M], LA [auth N], MA [auth O], NA [auth P], OA [auth Q], PA [auth R], QA [auth S], RA [auth T], SA [auth U], TA [auth V], UA [auth W], VA [auth X], Y [auth A], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain KA [auth M] Focus chain LA [auth N] Focus chain MA [auth O] Focus chain NA [auth P] Focus chain OA [auth Q] Focus chain PA [auth R] Focus chain QA [auth S] Focus chain RA [auth T] Focus chain SA [auth U] Focus chain TA [auth V] Focus chain UA [auth W] Focus chain VA [auth X] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain KA [auth M] Focus chain LA [auth N] Focus chain MA [auth O] Focus chain NA [auth P] Focus chain OA [auth Q] Focus chain PA [auth R] Focus chain QA [auth S] Focus chain RA [auth T] Focus chain SA [auth U] Focus chain TA [auth V] Focus chain UA [auth W] Focus chain VA [auth X] Focus chain Y [auth A] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.266
R-Value Work: 0.243
R-Value Observed: 0.244
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.395	α = 90
b = 217.612	β = 89.98
c = 146.266	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-02-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-02-25
Type: Initial release
Version 1.1: 2015-04-01
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Refinement description, Structure summary