1V0Z

Structure of Neuraminidase from English duck subtype N6

PDB DOI: https://doi.org/10.2210/pdb1V0Z/pdb

Classification: HYDROLASE
Organism(s): Influenza A virus
Expression System: Gallus gallus
Mutation(s): No

Deposited: 2004-03-12 Released: 2006-01-25
Deposition Author(s): Rudino-Pinera, E., Tunnah, P., Crennell, S.J., Webster, R.G., Laver, W.G., Garman, E.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.190
R-Value Work: 0.149
R-Value Observed: 0.151

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Literature

The Crystal Structure of Influenza Type a Virus Neuraminidase of the N6 Subtype at 1.85 A Resolution

Rudino-Pinera, E., Crennell, S.J., Webster, R.G., Laver, W.G., Garman, E.F.

To be published.

Macromolecule Content

Total Structure Weight: 180.11 kDa
Atom Count: 14,347
Modelled Residue Count: 1,556
Deposited Residue Count: 1,556
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEURAMINIDASE	A, B, C, D	389	Influenza A virus	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6XV27
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	4		N/A	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G00027MO GlyCosmos: G00027MO GlyGen: G00027MO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	6		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N/A	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G41734DZ GlyCosmos: G41734DZ GlyGen: G41734DZ

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose	J	2		N/A	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G71124KE GlyCosmos: G71124KE GlyGen: G71124KE

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 DA [auth C] SDF format, chain FA [auth D] SDF format, chain EA [auth C] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Z [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth C]	DA [auth C] EA [auth C] FA [auth D] IA [auth D] JA [auth D] DA [auth C], EA [auth C], FA [auth D], IA [auth D], JA [auth D], KA [auth D], M [auth A], N [auth A], Q [auth A], V [auth B], W [auth B], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain Z [auth C]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain LA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B]	LA [auth D] O [auth A] P [auth A] R [auth A] S [auth A] LA [auth D], O [auth A], P [auth A], R [auth A], S [auth A], X [auth B], Y [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain LA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain LA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain X [auth B] Focus chain Y [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] MOL2 format, chain BA [auth C]	BA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Interactions & Density Focus chain BA [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain CA [auth C] SDF format, chain L [auth A] SDF format, chain U [auth B] MOL2 format, chain HA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B]	CA [auth C], HA [auth D], L [auth A], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain HA [auth D] Focus chain L [auth A] Focus chain U [auth B] Interactions & Density Focus chain CA [auth C] Focus chain HA [auth D] Focus chain L [auth A] Focus chain U [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain T [auth B] SDF format, chain AA [auth C] SDF format, chain K [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain K [auth A]	AA [auth C], GA [auth D], K [auth A], T [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain K [auth A] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain K [auth A] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.190
R-Value Work: 0.149
R-Value Observed: 0.151
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.482	α = 90
b = 73.755	β = 90.37
c = 106.809	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-01-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-01-25
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2017-07-12
Changes: Advisory, Atomic model, Data collection, Derived calculations
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 3.1: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

1V0Z

Structure of Neuraminidase from English duck subtype N6

The Crystal Structure of Influenza Type a Virus Neuraminidase of the N6 Subtype at 1.85 A Resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)