6D96

Structure of influenza neuraminidase from strain A/BrevigMission/1/1918(H1N1) expressed in HEK-293E cells

PDB DOI: https://doi.org/10.2210/pdb6D96/pdb

Classification: HYDROLASE
Organism(s): Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2018-04-27 Released: 2019-05-01
Deposition Author(s): Campbell, A.C., Krause, K.L., Tanner, J.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.215
R-Value Work: 0.186
R-Value Observed: 0.187

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

Optimisation of neuraminidase expression by HEK-293E cells for use in structural biology

Campbell, A.C., Tanner, J.J., Krause, K.L.

To be published.

Macromolecule Content

Total Structure Weight: 364.19 kDa
Atom Count: 25,633
Modelled Residue Count: 3,088
Deposited Residue Count: 3,232
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, E A, B, C, D, E, F, G, H	404	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Mutation(s): 0 Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for Q9IGQ6 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9IGQ6 Go to UniProtKB: Q9IGQ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9IGQ6
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I, J, L, N, O	3		N-Glycosylation	Interactions Focus chain I Focus chain J Focus chain L Focus chain N Focus chain O Interactions & Density Focus chain I Focus chain J Focus chain L Focus chain N Focus chain O
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, M	2		N-Glycosylation	Interactions Focus chain K Focus chain M Interactions & Density Focus chain K Focus chain M
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth H] SDF format, chain BA [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth F] SDF format, chain R [auth A] SDF format, chain RA [auth F] SDF format, chain UA [auth G] SDF format, chain VA [auth G] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain ZA [auth H] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth F] MOL2 format, chain UA [auth G] MOL2 format, chain VA [auth G] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain ZA [auth H] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth H] mmCIF format, chain BA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain KA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth F] mmCIF format, chain UA [auth G] mmCIF format, chain VA [auth G] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain ZA [auth H]	AA [auth C] AB [auth H] BA [auth C] FA [auth D] GA [auth D] AA [auth C], AB [auth H], BA [auth C], FA [auth D], GA [auth D], KA [auth E], LA [auth E], P [auth A], Q [auth A], QA [auth F], R [auth A], RA [auth F], UA [auth G], VA [auth G], W [auth B], X [auth B], ZA [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth F] Focus chain R [auth A] Focus chain RA [auth F] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain W [auth B] Focus chain X [auth B] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth F] Focus chain R [auth A] Focus chain RA [auth F] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain W [auth B] Focus chain X [auth B] Focus chain ZA [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DB [auth H] SDF format, chain EA [auth C] SDF format, chain JA [auth D] SDF format, chain OA [auth E] SDF format, chain U [auth A] SDF format, chain YA [auth G] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain OA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain YA [auth G] mmCIF format, chain DB [auth H] mmCIF format, chain EA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain OA [auth E] mmCIF format, chain U [auth A] mmCIF format, chain YA [auth G]	DB [auth H] EA [auth C] JA [auth D] OA [auth E] U [auth A] DB [auth H], EA [auth C], JA [auth D], OA [auth E], U [auth A], YA [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DB [auth H] Focus chain EA [auth C] Focus chain JA [auth D] Focus chain OA [auth E] Focus chain U [auth A] Focus chain YA [auth G] Interactions & Density Focus chain DB [auth H] Focus chain EA [auth C] Focus chain JA [auth D] Focus chain OA [auth E] Focus chain U [auth A] Focus chain YA [auth G]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BB [auth H] SDF format, chain CA [auth C] SDF format, chain CB [auth H] SDF format, chain DA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain PA [auth E] SDF format, chain S [auth A] SDF format, chain SA [auth F] SDF format, chain T [auth A] SDF format, chain TA [auth F] SDF format, chain V [auth A] SDF format, chain WA [auth G] SDF format, chain XA [auth G] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain BB [auth H] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth H] MOL2 format, chain DA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth F] MOL2 format, chain V [auth A] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain BB [auth H] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth H] mmCIF format, chain DA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain MA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth F] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth F] mmCIF format, chain V [auth A] mmCIF format, chain WA [auth G] mmCIF format, chain XA [auth G] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	BB [auth H] CA [auth C] CB [auth H] DA [auth C] HA [auth D] BB [auth H], CA [auth C], CB [auth H], DA [auth C], HA [auth D], IA [auth D], MA [auth E], NA [auth E], PA [auth E], S [auth A], SA [auth F], T [auth A], TA [auth F], V [auth A], WA [auth G], XA [auth G], Y [auth B], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BB [auth H] Focus chain CA [auth C] Focus chain CB [auth H] Focus chain DA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain PA [auth E] Focus chain S [auth A] Focus chain SA [auth F] Focus chain T [auth A] Focus chain TA [auth F] Focus chain V [auth A] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain BB [auth H] Focus chain CA [auth C] Focus chain CB [auth H] Focus chain DA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain PA [auth E] Focus chain S [auth A] Focus chain SA [auth F] Focus chain T [auth A] Focus chain TA [auth F] Focus chain V [auth A] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.215
R-Value Work: 0.186
R-Value Observed: 0.187
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.681	α = 90
b = 148.189	β = 94.8
c = 127.166	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-05-01

Deposition Author(s):

Campbell, A.C.

Krause, K.L.

Tanner, J.J.

Revision History (Full details and data files)

Version 1.0: 2019-05-01
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: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-23
Changes: Structure summary