Macromolecule Content

Total Structure Weight: 181.19 kDa
Atom Count: 15100
Modelled Residue Count: 1556
Deposited Residue Count: 1556
Unique protein chains: 1

6HG5

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

PDB DOI: 10.2210/pdb6HG5/pdb

Classification: HYDROLASE
Organism(s): Influenza A virus (A/duck/England/1/1956(H11N6))
Expression System: Gallus gallus
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: 1.60 Å
R-Value Free: 0.158
R-Value Work: 0.133
R-Value Observed: 0.134

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

High Resolution Structures of Viral Neuraminidase with Drugs Bound in the Active Site.

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

To be published.

Macromolecules

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(by identity cutoff) | 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 Gene Names: NA 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6XV27
Protein Feature View Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, I, K	2		N-Glycosylation	Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D 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, H	7		N-Glycosylation	Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D 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	J, L	6		N-Glycosylation	Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan: G94106MV GlyCosmos: G94106MV GlyGen: G94106MV

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G39 Query on G39 Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain X [auth C] SDF format, chain N [auth A] SDF format, chain Q [auth B] MOL2 format, chain CA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B]	CA [auth D], N [auth A], Q [auth B], X [auth C]	(3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid C₁₄ H₂₄ N₂ O₄ NENPYTRHICXVCS-YNEHKIRRSA-N		Ligand Interaction
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain W [auth C] SDF format, chain BA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain W [auth C] MOL2 format, chain BA [auth D]	BA [auth D], M [auth A], W [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Y [auth C] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain R [auth B] SDF format, chain U [auth B] SDF format, chain Z [auth C] MOL2 format, chain O [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Z [auth C]	DA [auth D], EA [auth D], O [auth A], R [auth B], S [auth B], DA [auth D], EA [auth D], O [auth A], R [auth B], S [auth B], T [auth B], U [auth B], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
CO2 Query on CO2 Download Ideal Coordinates CCD File SDF format, chain GA [auth D] MOL2 format, chain GA [auth D]	GA [auth D]	CARBON DIOXIDE C O₂ CURLTUGMZLYLDI-UHFFFAOYSA-N		Ligand Interaction
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain V [auth B] SDF format, chain AA [auth C] SDF format, chain P [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain P [auth A]	AA [auth C], FA [auth D], P [auth A], V [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
G39	BindingDB: 6HG5	IC50: 15 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.158
R-Value Work: 0.133
R-Value Observed: 0.134
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.209	α = 90
b = 75.181	β = 90.52
c = 106.386	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Deposited Date: 2018-08-22
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