1V0Z | pdb_00001v0z

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 (Depositor), 0.187 (DCC)
R-Value Work:
0.149 (Depositor), 0.150 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 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
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	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
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, 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	D 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	D 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	D 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	D 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 EA [auth C] SDF format, chain FA [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 Z [auth C] SDF format, chain W [auth B] SDF format, chain IA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [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 Z [auth C] MOL2 format, chain W [auth B] MOL2 format, chain IA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain V [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain W [auth B] mmCIF format, chain IA [auth D]	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 R [auth A] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain S [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain LA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain S [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain LA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain S [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain LA [auth D]	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] mmCIF 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 U [auth B] SDF format, chain L [auth A] SDF format, chain HA [auth D] SDF format, chain CA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain L [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain CA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain L [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain CA [auth C]	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 T [auth B] SDF format, chain K [auth A] SDF format, chain GA [auth D] SDF format, chain AA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain AA [auth C]	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 (Depositor), 0.187 (DCC)
R-Value Work: 0.149 (Depositor), 0.150 (DCC)
R-Value Observed: 0.151 (Depositor)

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

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Ligand Structure Quality Assessment

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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
Version 3.2: 2024-10-23
Changes: Structure summary