4B7Q

H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis

PDB DOI: https://doi.org/10.2210/pdb4B7Q/pdb

Classification: HYDROLASE
Organism(s): Influenza A virus (A/California/07/2009(H1N1))
Mutation(s): No

Deposited: 2012-08-21 Released: 2012-10-03
Deposition Author(s): Liu, J., van der Vries, E., Vachieri, S.G., Xiong, X., Collins, P.J., Walker, P.A., Haire, L.F., Hay, A.J., Schutten, M., Osterhaus, A.D.M.E., Martin, S.R., Boucher, C.A.B., Skehel, J.J., Gamblin, S.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free: 0.258
R-Value Work: 0.174
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 209.85 kDa
Atom Count: 12,571
Modelled Residue Count: 1,548
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/California/07/2009(H1N1))	Mutation(s): 0
UniProt
Find proteins for C7FH46 (Influenza A virus) Explore C7FH46 Go to UniProtKB: C7FH46
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7FH46
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZMR Query on ZMR Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D]	F [auth A], K [auth B], P [auth C], T [auth D]	ZANAMIVIR C₁₂ H₂₀ N₄ O₇ ARAIBEBZBOPLMB-UFGQHTETSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain S [auth D]	E [auth A] I [auth B] J [auth B] M [auth C] N [auth C] E [auth A], I [auth B], J [auth B], M [auth C], N [auth C], O [auth C], R [auth D], S [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain U [auth D] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain U [auth D]	G [auth A], H [auth A], L [auth B], Q [auth C], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
ZMR	PDBBind: 4B7Q	Ki: 0.18 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free: 0.258
R-Value Work: 0.174
R-Value Observed: 0.178
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.65	α = 90
b = 148.82	β = 90
c = 166.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-03
Type: Initial release
Version 1.1: 2012-10-10
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary