4MZE

Crystal structure of hPIV3 hemagglutinin-neuraminidase, H552Q/Q559R mutant

PDB DOI: https://doi.org/10.2210/pdb4MZE/pdb

Classification: HYDROLASE
Organism(s): Human parainfluenza 3 virus (strain NIH 47885)
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2013-09-30 Released: 2013-11-06
Deposition Author(s): Xu, R., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.196
R-Value Work: 0.161
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 103.17 kDa
Atom Count: 7,803
Modelled Residue Count: 864
Deposited Residue Count: 874
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin-neuraminidase	A, B	437	Human parainfluenza 3 virus (strain NIH 47885)	Mutation(s): 2 Gene Names: HN EC: 3.2.1.18
UniProt
Find proteins for P08492 (Human parainfluenza 3 virus (strain Wash/47885/57)) Explore P08492 Go to UniProtKB: P08492
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08492
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	8		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G61843VN GlyCosmos: G61843VN GlyGen: G61843VN

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	5		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain U [auth B] MOL2 format, chain G [auth A] MOL2 format, chain U [auth B]	G [auth A], U [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain U [auth B] Interactions & Density Focus chain G [auth A] Focus chain U [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A]	FA [auth B], GA [auth B], R [auth A], S [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain R [auth A] Focus chain S [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A]	T [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain H [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	H [auth A], V [auth B], W [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain H [auth A] Focus chain V [auth B] Focus chain W [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain X [auth B] MOL2 format, chain I [auth A] MOL2 format, chain X [auth B]	I [auth A], X [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain X [auth B] Interactions & Density Focus chain I [auth A] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.196
R-Value Work: 0.161
R-Value Observed: 0.163
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.029	α = 90
b = 96.643	β = 90
c = 105.339	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-11-06

Deposition Author(s):

Xu, R.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2013-11-06
Type: Initial release
Version 1.1: 2014-08-27
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary