3K3A

Crystal Structure of B/Perth Neuraminidase D197E mutant in complex with Oseltamivir

PDB DOI: https://doi.org/10.2210/pdb3K3A/pdb

Classification: HYDROLASE
Organism(s): Influenza B virus (B/Perth/211/2001)
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2009-10-02 Released: 2010-09-01
Deposition Author(s): Oakley, A.J., McKimm-Breschkin, J.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.229
R-Value Work: 0.207
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 710.51 kDa
Atom Count: 49,183
Modelled Residue Count: 6,224
Deposited Residue Count: 6,352
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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, I, J, K, L, M, N, O, P	397	Influenza B virus (B/Perth/211/2001)	Mutation(s): 1 EC: 3.2.1.18
UniProt
Find proteins for Q3S340 (Influenza B virus) Explore Q3S340 Go to UniProtKB: Q3S340
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3S340
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G39 Query on G39 Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain CB [auth L] SDF format, chain FB [auth M] SDF format, chain GA [auth E] SDF format, chain IB [auth N] SDF format, chain JA [auth F] SDF format, chain LB [auth O] SDF format, chain MA [auth G] SDF format, chain PA [auth H] SDF format, chain PB [auth P] SDF format, chain S [auth A] SDF format, chain SA [auth I] SDF format, chain W [auth B] SDF format, chain WA [auth J] SDF format, chain Z [auth C] SDF format, chain ZA [auth K] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth L] MOL2 format, chain FB [auth M] MOL2 format, chain GA [auth E] MOL2 format, chain IB [auth N] MOL2 format, chain JA [auth F] MOL2 format, chain LB [auth O] MOL2 format, chain MA [auth G] MOL2 format, chain PA [auth H] MOL2 format, chain PB [auth P] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth I] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth J] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth K]	CA [auth D] CB [auth L] FB [auth M] GA [auth E] IB [auth N] CA [auth D], CB [auth L], FB [auth M], GA [auth E], IB [auth N], JA [auth F], LB [auth O], MA [auth G], PA [auth H], PB [auth P], S [auth A], SA [auth I], W [auth B], WA [auth J], Z [auth C], ZA [auth K]	(3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid C₁₄ H₂₄ N₂ O₄ NENPYTRHICXVCS-YNEHKIRRSA-N		Interactions Focus chain CA [auth D] Focus chain CB [auth L] Focus chain FB [auth M] Focus chain GA [auth E] Focus chain IB [auth N] Focus chain JA [auth F] Focus chain LB [auth O] Focus chain MA [auth G] Focus chain PA [auth H] Focus chain PB [auth P] Focus chain S [auth A] Focus chain SA [auth I] Focus chain W [auth B] Focus chain WA [auth J] Focus chain Z [auth C] Focus chain ZA [auth K] Interactions & Density Focus chain CA [auth D] Focus chain CB [auth L] Focus chain FB [auth M] Focus chain GA [auth E] Focus chain IB [auth N] Focus chain JA [auth F] Focus chain LB [auth O] Focus chain MA [auth G] Focus chain PA [auth H] Focus chain PB [auth P] Focus chain S [auth A] Focus chain SA [auth I] Focus chain W [auth B] Focus chain WA [auth J] Focus chain Z [auth C] Focus chain ZA [auth K]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth L] SDF format, chain DB [auth M] SDF format, chain EA [auth E] SDF format, chain GB [auth N] SDF format, chain HA [auth F] SDF format, chain JB [auth O] SDF format, chain KA [auth G] SDF format, chain NA [auth H] SDF format, chain NB [auth P] SDF format, chain Q [auth A] SDF format, chain QA [auth I] SDF format, chain U [auth B] SDF format, chain UA [auth J] SDF format, chain X [auth C] SDF format, chain XA [auth K] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth L] MOL2 format, chain DB [auth M] MOL2 format, chain EA [auth E] MOL2 format, chain GB [auth N] MOL2 format, chain HA [auth F] MOL2 format, chain JB [auth O] MOL2 format, chain KA [auth G] MOL2 format, chain NA [auth H] MOL2 format, chain NB [auth P] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth I] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth J] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth K]	AA [auth D] AB [auth L] DB [auth M] EA [auth E] GB [auth N] AA [auth D], AB [auth L], DB [auth M], EA [auth E], GB [auth N], HA [auth F], JB [auth O], KA [auth G], NA [auth H], NB [auth P], Q [auth A], QA [auth I], U [auth B], UA [auth J], X [auth C], XA [auth K]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth L] Focus chain DB [auth M] Focus chain EA [auth E] Focus chain GB [auth N] Focus chain HA [auth F] Focus chain JB [auth O] Focus chain KA [auth G] Focus chain NA [auth H] Focus chain NB [auth P] Focus chain Q [auth A] Focus chain QA [auth I] Focus chain U [auth B] Focus chain UA [auth J] Focus chain X [auth C] Focus chain XA [auth K] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth L] Focus chain DB [auth M] Focus chain EA [auth E] Focus chain GB [auth N] Focus chain HA [auth F] Focus chain JB [auth O] Focus chain KA [auth G] Focus chain NA [auth H] Focus chain NB [auth P] Focus chain Q [auth A] Focus chain QA [auth I] Focus chain U [auth B] Focus chain UA [auth J] Focus chain X [auth C] Focus chain XA [auth K]
YT3 Query on YT3 Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain MB [auth P] SDF format, chain T [auth A] SDF format, chain TA [auth J] MOL2 format, chain DA [auth E] MOL2 format, chain MB [auth P] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth J]	DA [auth E], MB [auth P], T [auth A], TA [auth J]	YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain MB [auth P] Focus chain T [auth A] Focus chain TA [auth J] Interactions & Density Focus chain DA [auth E] Focus chain MB [auth P] Focus chain T [auth A] Focus chain TA [auth J]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain BB [auth L] SDF format, chain EB [auth M] SDF format, chain FA [auth E] SDF format, chain HB [auth N] SDF format, chain IA [auth F] SDF format, chain KB [auth O] SDF format, chain LA [auth G] SDF format, chain OA [auth H] SDF format, chain OB [auth P] SDF format, chain R [auth A] SDF format, chain RA [auth I] SDF format, chain V [auth B] SDF format, chain VA [auth J] SDF format, chain Y [auth C] SDF format, chain YA [auth K] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth L] MOL2 format, chain EB [auth M] MOL2 format, chain FA [auth E] MOL2 format, chain HB [auth N] MOL2 format, chain IA [auth F] MOL2 format, chain KB [auth O] MOL2 format, chain LA [auth G] MOL2 format, chain OA [auth H] MOL2 format, chain OB [auth P] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth I] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth J] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth K]	BA [auth D] BB [auth L] EB [auth M] FA [auth E] HB [auth N] BA [auth D], BB [auth L], EB [auth M], FA [auth E], HB [auth N], IA [auth F], KB [auth O], LA [auth G], OA [auth H], OB [auth P], R [auth A], RA [auth I], V [auth B], VA [auth J], Y [auth C], YA [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain BB [auth L] Focus chain EB [auth M] Focus chain FA [auth E] Focus chain HB [auth N] Focus chain IA [auth F] Focus chain KB [auth O] Focus chain LA [auth G] Focus chain OA [auth H] Focus chain OB [auth P] Focus chain R [auth A] Focus chain RA [auth I] Focus chain V [auth B] Focus chain VA [auth J] Focus chain Y [auth C] Focus chain YA [auth K] Interactions & Density Focus chain BA [auth D] Focus chain BB [auth L] Focus chain EB [auth M] Focus chain FA [auth E] Focus chain HB [auth N] Focus chain IA [auth F] Focus chain KB [auth O] Focus chain LA [auth G] Focus chain OA [auth H] Focus chain OB [auth P] Focus chain R [auth A] Focus chain RA [auth I] Focus chain V [auth B] Focus chain VA [auth J] Focus chain Y [auth C] Focus chain YA [auth K]

Binding Affinity Annotations
ID	Source	Binding Affinity
G39	PDBBind: 3K3A	Ki: 84 (nM) from 1 assay(s)
	BindingDB: 3K3A	Ki: 1.1 (nM) from 1 assay(s)
	BindingDB: 3K3A	IC50: min: 3, max: 61 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.229
R-Value Work: 0.207
R-Value Observed: 0.208
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.802	α = 90.04
b = 123.836	β = 90.17
c = 123.967	γ = 90.1

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-09-01

Deposition Author(s):

Oakley, A.J.

McKimm-Breschkin, J.L.

Revision History (Full details and data files)

Version 1.0: 2010-09-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2021-11-10
Changes: Database references, Structure summary
Version 1.4: 2023-11-01
Changes: Data collection, Refinement description