1W21 | pdb_00001w21

Structure of Neuraminidase from English duck subtype N6 complexed with 30 mM sialic acid (NANA, Neu5Ac), crystal soaked for 43 hours at 291 K.

PDB DOI: https://doi.org/10.2210/pdb1W21/pdb

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

Deposited: 2004-06-25 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: 2.08 Å
R-Value Free:
0.195 (Depositor), 0.208 (DCC)
R-Value Work:
0.150 (Depositor), 0.161 (DCC)
R-Value Observed:
0.153 (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: 180.32 kDa
Atom Count: 14,285
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: 1	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, F, H	2		N/A	Interactions Focus chain E Focus chain F Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA Query on SIA Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain J [auth A] SDF format, chain MA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain LA [auth D] SDF format, chain I [auth A] SDF format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain LA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain BA [auth C]	BA [auth C] CA [auth C] I [auth A] J [auth A] LA [auth D] BA [auth C], CA [auth C], I [auth A], J [auth A], LA [auth D], MA [auth D], S [auth B], T [auth B]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain S [auth B] Focus chain T [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain OA [auth D] SDF format, chain V [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain V [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain V [auth B]	EA [auth C], L [auth A], M [auth A], OA [auth D], 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 L [auth A] Focus chain M [auth A] Focus chain OA [auth D] Focus chain V [auth B] Interactions & Density Focus chain EA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain OA [auth D] Focus chain V [auth B]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain O [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain Q [auth A] SDF format, chain P [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A]	FA [auth C] GA [auth C] HA [auth C] IA [auth C] O [auth A] FA [auth C], GA [auth C], HA [auth C], IA [auth C], O [auth A], P [auth A], Q [auth A], X [auth B], Y [auth B], Z [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain W [auth B] SDF format, chain JA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain W [auth B] MOL2 format, chain JA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain W [auth B] mmCIF format, chain JA [auth C]	JA [auth C], N [auth A], W [auth B]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain JA [auth C] Focus chain N [auth A] Focus chain W [auth B] Interactions & Density Focus chain JA [auth C] Focus chain N [auth A] Focus chain W [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain NA [auth D] SDF format, chain U [auth B] SDF format, chain DA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain DA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain DA [auth C]	DA [auth C], K [auth A], NA [auth D], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain K [auth A] Focus chain NA [auth D] Focus chain U [auth B] Interactions & Density Focus chain DA [auth C] Focus chain K [auth A] Focus chain NA [auth D] Focus chain U [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain PA [auth D] SDF format, chain KA [auth C] SDF format, chain AA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain KA [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain KA [auth C] mmCIF format, chain AA [auth B]	AA [auth B], KA [auth C], PA [auth D], R [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain KA [auth C] Focus chain PA [auth D] Focus chain R [auth A] Interactions & Density Focus chain AA [auth B] Focus chain KA [auth C] Focus chain PA [auth D] Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.195 (Depositor), 0.208 (DCC)
R-Value Work: 0.150 (Depositor), 0.161 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.478	α = 90
b = 73.995	β = 90.5
c = 106.465	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	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 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: 2024-11-13
Changes: Structure summary