6HGB | pdb_00006hgb

Influenza A virus N6 neuraminidase native structure (Duck/England/56).

PDB DOI: https://doi.org/10.2210/pdb6HGB/pdb

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

Deposited: 2018-08-23 Released: 2018-09-05
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: 1.50 Å
R-Value Free:
0.161 (Depositor), 0.163 (DCC)
R-Value Work:
0.139 (Depositor), 0.141 (DCC)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
View more details

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: 184.58 kDa
Atom Count: 15,249
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: 3	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, F, H, J, K E, F, H, J, K, N	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain H Focus chain J Focus chain K Focus chain N Interactions & Density Focus chain E Focus chain F Focus chain H Focus chain J Focus chain K Focus chain N
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	G	8		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

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)-[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	I	7		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 5
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	L, M	6		N-Glycosylation	Interactions Focus chain L Focus chain M Interactions & Density Focus chain L Focus chain M
Glycosylation Resources
GlyTouCan: G94106MV GlyCosmos: G94106MV GlyGen: G94106MV

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain CB [auth D] SDF format, chain Y [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain Y [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain Y [auth B]	CB [auth D], Y [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CB [auth D] Focus chain Y [auth B] Interactions & Density Focus chain CB [auth D] Focus chain Y [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain JB [auth D] SDF format, chain KA [auth B] SDF format, chain KB [auth D] SDF format, chain LB [auth D] SDF format, chain MA [auth B] SDF format, chain MB [auth D] SDF format, chain NA [auth B] SDF format, chain NB [auth D] SDF format, chain OA [auth B] SDF format, chain OB [auth D] SDF format, chain X [auth A] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] SDF format, chain LA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain LB [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth D] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain X [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain LA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth D] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth D] mmCIF format, chain LB [auth D] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth D] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth D] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth D] mmCIF format, chain X [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain LA [auth B]	AB [auth C] BB [auth C] HA [auth B] IA [auth B] JA [auth B] AB [auth C], BB [auth C], HA [auth B], IA [auth B], JA [auth B], JB [auth D], KA [auth B], KB [auth D], LA [auth B], LB [auth D], MA [auth B], MB [auth D], NA [auth B], NB [auth D], OA [auth B], OB [auth D], X [auth A], YA [auth C], ZA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain X [auth A] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain X [auth A] Focus chain YA [auth C] Focus chain ZA [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A]	GA [auth B], V [auth A], W [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain GA [auth B] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain GA [auth B] Focus chain V [auth A] Focus chain W [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain GB [auth D] SDF format, chain HB [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain HB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain GB [auth D] mmCIF format, chain HB [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] DB [auth D] AA [auth B], BA [auth B], CA [auth B], DA [auth B], DB [auth D], EA [auth B], EB [auth D], FB [auth D], GB [auth D], HB [auth D], O [auth A], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], UA [auth C], VA [auth C], WA [auth C], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain Z [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain IB [auth D] SDF format, chain U [auth A] SDF format, chain XA [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain IB [auth D] MOL2 format, chain U [auth A] MOL2 format, chain XA [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain IB [auth D] mmCIF format, chain U [auth A] mmCIF format, chain XA [auth C]	FA [auth B], IB [auth D], U [auth A], XA [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain IB [auth D] Focus chain U [auth A] Focus chain XA [auth C] Interactions & Density Focus chain FA [auth B] Focus chain IB [auth D] Focus chain U [auth A] Focus chain XA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.161 (Depositor), 0.163 (DCC)
R-Value Work: 0.139 (Depositor), 0.141 (DCC)
R-Value Observed: 0.140 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.2	α = 90
b = 73.9	β = 90.3
c = 106.4	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

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-09-05

Deposition Author(s):

Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2018-09-05
Type: Initial release
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: 2024-11-06
Changes: Structure summary