5W2W

INFLUENZA VIRUS NEURAMINIDASE N9 IN COMPLEX WITH 8-DEOXYGENATED 2,3-DIFLUORO-N-ACETYLNEURAMINIC ACID

PDB DOI: https://doi.org/10.2210/pdb5W2W/pdb

Classification: hydrolase/hydrolase inhibitor
Organism(s): Influenza A virus (A/tern/Australia/G70C/1975(H11N9))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2017-06-07 Released: 2018-02-21
Deposition Author(s): Streltsov, V.A., Mckimm-Breschkin, J., Barrett, S., Pilling, P., Hader, S., Watt, A.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.171
R-Value Work: 0.140
R-Value Observed: 0.142

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: 46.87 kDa
Atom Count: 3,779
Modelled Residue Count: 388
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A	388	Influenza A virus (A/tern/Australia/G70C/1975(H11N9))	Mutation(s): 0 Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9)) Explore P03472 Go to UniProtKB: P03472
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03472
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	9		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G68668TB GlyCosmos: G68668TB GlyGen: G68668TB

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9SP Query on 9SP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	(2R,3R,4R,5R,6R)-5-acetamido-6-[(1R)-1,3-bis(oxidanyl)propyl]-2,3-bis(fluoranyl)-4-oxidanyl-oxane-2-carboxylic acid C₁₁ H₁₇ F₂ N O₇ SVILRGMXTMNWJP-XYLHZXCYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
9S7 Query on 9S7 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	5-acetamido-2,6-anhydro-3,5,8-trideoxy-3-fluoro-D-threo-L-galacto-nononic acid C₁₁ H₁₈ F N O₇ MCQSBVLYLCZSNU-AIGBEWNKSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
9SD Query on 9SD Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	(2~{R},3~{R},4~{R},5~{R})-3-acetamido-2-[(1~{R})-1,3-bis(oxidanyl)propyl]-5-fluoranyl-4-oxidanyl-2,3,4,5-tetrahydropyran-1-ium-6-carboxylic acid C₁₁ H₁₇ F N O₇ CHPKCUSAUNABPC-HXLXBVJFSA-O		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.171
R-Value Work: 0.140
R-Value Observed: 0.142
Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.709	α = 90
b = 180.709	β = 90
c = 180.709	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-02-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-02-21
Type: Initial release
Version 1.1: 2018-03-21
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: 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