5VTW

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin G225M/L226T/S228A mutant in complex with 6'-SLN

PDB DOI: https://doi.org/10.2210/pdb5VTW/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Hong Kong/1/1968(H3N2))
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2017-05-18 Released: 2017-06-28
Deposition Author(s): Wu, N.C., Wilson, I.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.213
R-Value Work: 0.193
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 172.88 kDa
Atom Count: 12,410
Modelled Residue Count: 1,469
Deposited Residue Count: 1,491
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	323	Influenza A virus (A/Hong Kong/1/1968(H3N2))	Mutation(s): 3 Gene Names: HA
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Explore Q91MA7 Go to UniProtKB: Q91MA7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91MA7
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	174	Influenza A virus (A/Hong Kong/1/1968(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Explore Q91MA7 Go to UniProtKB: Q91MA7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91MA7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, J	3		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain J Interactions & Density Focus chain G Focus chain H Focus chain J
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, K	2		N-Glycosylation	Interactions Focus chain I Focus chain K Interactions & Density Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose	L, N	2		N/A	Interactions Focus chain L Focus chain N Interactions & Density Focus chain L Focus chain N
Glycosylation Resources
GlyTouCan: G63069TR GlyCosmos: G63069TR GlyGen: G63069TR

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M	4		N-Glycosylation	Interactions Focus chain M Interactions & Density Focus chain M
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA Query on SIA Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A]	P [auth A]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain V [auth F] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F]	O [auth A] Q [auth C] R [auth C] S [auth E] T [auth E] O [auth A], Q [auth C], R [auth C], S [auth E], T [auth E], V [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain O [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Interactions & Density Focus chain O [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F]
TAM Query on TAM Download Ideal Coordinates CCD File SDF format, chain U [auth E] MOL2 format, chain U [auth E]	U [auth E]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain U [auth E] Interactions & Density Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.213
R-Value Work: 0.193
R-Value Observed: 0.194
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.65	α = 90
b = 131.53	β = 98.05
c = 72.728	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-06-28

Deposition Author(s):

Wu, N.C.

Wilson, I.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R56 AI117675
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI114730

Revision History (Full details and data files)

Version 1.0: 2017-06-28
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Refinement description
Version 1.2: 2019-12-11
Changes: Author supporting evidence, Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary