1W1X

Structure of Neuraminidase from English duck subtype N6 complexed with 30 mM sialic acid (NANA, Neu5Ac), crystal soaked for 3 hours at 277 K.

PDB DOI: https://doi.org/10.2210/pdb1W1X/pdb

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

Deposited: 2004-06-24 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: 2.00 ?
R-Value Free:
0.207 (Depositor), 0.180 (DCC)
R-Value Work:
0.164 (Depositor), 0.170 (DCC)
R-Value Observed:
0.167 (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

The Crystal Structure of Type a Influenza Virus Neuraminidase of the N6 Subtype Reveals the Existence of Two Separate Neu5Ac Binding Sites

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

To be published.

Macromolecule Content

Total Structure Weight: 180.17 kDa
Atom Count: 14,123
Modelled Residue Count: 1,556
Deposited Residue Count: 1,556
Unique protein chains: 1

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	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
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	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose	E	3		N/A	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G91725EU GlyCosmos: G91725EU GlyGen: G91725EU

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	3		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose	H	2		N/A	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G77384RA GlyCosmos: G77384RA GlyGen: G77384RA

Entity ID: 6
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	I	3		N/A	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G41734DZ GlyCosmos: G41734DZ GlyGen: G41734DZ

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA Query on SIA Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain HA [auth D] SDF format, chain S [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain S [auth B] mmCIF format, chain GA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain S [auth B]	GA [auth D] HA [auth D] K [auth A] L [auth A] R [auth B] GA [auth D], HA [auth D], K [auth A], L [auth A], R [auth B], S [auth B], Y [auth C], Z [auth C]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain GA [auth D] Focus chain HA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain HA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain KA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain V [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain V [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain V [auth B]	EA [auth C], KA [auth D], O [auth A], P [auth A], V [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain EA [auth C] Focus chain KA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B] Interactions & Density Focus chain EA [auth C] Focus chain KA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B]
BMA Query on BMA Download Ideal Coordinates CCD File SDF format, chain JA [auth D] MOL2 format, chain JA [auth D] mmCIF format, chain JA [auth D]	JA [auth D]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain JA [auth D] Interactions & Density Focus chain JA [auth D]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain U [auth B] SDF format, chain DA [auth C] SDF format, chain N [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain N [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain N [auth A]	BA [auth C], CA [auth C], DA [auth C], N [auth A], U [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain N [auth A] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain N [auth A] Focus chain U [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C] mmCIF format, chain X [auth C]	X [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain LA [auth D] SDF format, chain W [auth B] SDF format, chain Q [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain Q [auth A]	FA [auth C], LA [auth D], Q [auth A], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain LA [auth D] Focus chain Q [auth A] Focus chain W [auth B] Interactions & Density Focus chain FA [auth C] Focus chain LA [auth D] Focus chain Q [auth A] Focus chain W [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain IA [auth D] SDF format, chain M [auth A] SDF format, chain T [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain T [auth B]	AA [auth C], IA [auth D], M [auth A], T [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain IA [auth D] Focus chain M [auth A] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain IA [auth D] Focus chain M [auth A] Focus chain T [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900118 Query on PRD_900118	H	6alpha-alpha-mannobiose	Oligosaccharide / Metabolism		Interactions Focus chain H Interactions & Density Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 ?
R-Value Free: 0.207 (Depositor), 0.180 (DCC)
R-Value Work: 0.164 (Depositor), 0.170 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 106.993	α = 90
b = 73.464	β = 90.38
c = 107.413	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	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 1.3: 2019-03-06
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary