3TIB

Crystal structure of 1957 pandemic H2N2 neuraminidase complexed with laninamivir octanoate

PDB DOI: https://doi.org/10.2210/pdb3TIB/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Influenza A virus (A/RI/5+/1957(H2N2))
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2011-08-20 Released: 2011-11-16
Deposition Author(s): Vavricka, C.J., Li, Q., Wu, Y., Qi, J., Wang, M., Liu, Y., Gao, F., Liu, J., Feng, E., He, J., Wang, J., Liu, H., Jiang, H., Gao, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.191
R-Value Work: 0.155
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 215.03 kDa
Atom Count: 13,900
Modelled Residue Count: 1,552
Deposited Residue Count: 1,876
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	469	Influenza A virus (A/RI/5+/1957(H2N2))	Mutation(s): 0
UniProt
Find proteins for Q194T1 (Influenza A virus) Explore Q194T1 Go to UniProtKB: Q194T1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q194T1
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)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, I, K	2		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain I Focus chain K Interactions & Density Focus chain E Focus chain G Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H, J, L	4		N-Glycosylation	Interactions Focus chain F Focus chain H Focus chain J Focus chain L Interactions & Density Focus chain F Focus chain H Focus chain J Focus chain L
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LVO Query on LVO Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D]	N [auth A], P [auth B], R [auth C], T [auth D]	5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-9-O-octanoyl-D-glycero-D-galacto-non-2-enonic acid C₂₁ H₃₆ N₄ O₈ UKTIJASCFRNWCB-RMIBSVFLSA-N		Interactions Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Interactions & Density Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain M [auth A]	M [auth A], O [auth B], Q [auth C], S [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Interactions & Density Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
LVO	Binding MOAD: 3TIB	IC50: 129 (nM) from 1 assay(s)
LVO	PDBBind: 3TIB	IC50: 129 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.191
R-Value Work: 0.155
R-Value Observed: 0.157
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.454	α = 90
b = 140.18	β = 101.22
c = 90.298	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-11-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-16
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary

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3TIB

Crystal structure of 1957 pandemic H2N2 neuraminidase complexed with laninamivir octanoate

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources