6HFY | pdb_00006hfy

Influenza A virus N6 neuraminidase complex with DANA (Duck/England/56).

PDB DOI: https://doi.org/10.2210/pdb6HFY/pdb

Classification: HYDROLASE
Organism(s): Influenza A virus (A/duck/England/1/1956(H11N6))
Mutation(s): No

Deposited: 2018-08-22 Released: 2018-08-29
Deposition Author(s): Salinger, M.T., Hobbs, J.R., Murray, J.W., Laver, W.G., Kuhn, P., Garman, E.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.185 (Depositor), 0.194 (DCC)
R-Value Work:
0.156 (Depositor), 0.167 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

High Resolution Structures of Viral Neuraminidase with Drugs Bound in the Active Site. (In preparation)

Salinger, M.T., Hobbs, J.R., Murray, J.W., Laver, W.G., Kuhn, P., Garman, E.F.

To be published.

Macromolecule Content

Total Structure Weight: 180.65 kDa
Atom Count: 14,206
Modeled Residue Count: 1,556
Deposited Residue Count: 1,556
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A, B, C, D	389	Influenza A virus (A/duck/England/1/1956(H11N6))	Mutation(s): 0 EC: 3.2.1.18
UniProt
Find proteins for Q6XV27 (Influenza A virus (strain A/Duck/England/1/1956 H11N6)) Explore Q6XV27 Go to UniProtKB: Q6XV27
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6XV27
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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	F	7		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	H, I, J	6		N-Glycosylation	Interactions Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain H Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G94106MV GlyCosmos: G94106MV GlyGen: G94106MV

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DAN Query on DAN Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain Q [auth B] SDF format, chain L [auth A] SDF format, chain DA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain L [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain L [auth A] mmCIF format, chain DA [auth D]	DA [auth D], L [auth A], Q [auth B], Y [auth C]	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID C₁₁ H₁₇ N O₈ JINJZWSZQKHCIP-UFGQHTETSA-N		Interactions Focus chain DA [auth D] Focus chain L [auth A] Focus chain Q [auth B] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain L [auth A] Focus chain Q [auth B] Focus chain Y [auth C]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain P [auth B] SDF format, chain K [auth A] SDF format, chain CA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A] mmCIF format, chain CA [auth D]	CA [auth D], K [auth A], P [auth B], W [auth C], X [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth D] Focus chain K [auth A] Focus chain P [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain K [auth A] Focus chain P [auth B] Focus chain W [auth C] Focus chain X [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain FA [auth D] SDF format, chain EA [auth D] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain AA [auth C]	AA [auth C] EA [auth D] FA [auth D] M [auth A] N [auth A] AA [auth C], EA [auth D], FA [auth D], M [auth A], N [auth A], R [auth B], S [auth B], T [auth B], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain O [auth A] SDF format, chain GA [auth D] SDF format, chain BA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain O [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain BA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain O [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain BA [auth C]	BA [auth C], GA [auth D], O [auth A], U [auth B], V [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain GA [auth D] Focus chain O [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain BA [auth C] Focus chain GA [auth D] Focus chain O [auth A] Focus chain U [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.185 (Depositor), 0.194 (DCC)
R-Value Work: 0.156 (Depositor), 0.167 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.995	α = 90
b = 75.763	β = 90.5
c = 105.976	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-08-29

Deposition Author(s):

Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2018-08-29
Type: Initial release
Version 1.1: 2018-09-05
Changes: Data collection, Database references, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary