4JUL

Crystal structure of H5N1 influenza virus hemagglutinin, clade 2.3.4

PDB DOI: https://doi.org/10.2210/pdb4JUL/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/duck/Laos/3295/2006(H5N1))
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2013-03-25 Released: 2014-05-07
Deposition Author(s): DuBois, R.M., Zaraket, H., Reddivari, M., Coop, T., Heath, R.J., White, S.W., Russell, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.254
R-Value Work: 0.196
R-Value Observed: 0.199

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: 350.56 kDa
Atom Count: 23,752
Modelled Residue Count: 2,950
Deposited Residue Count: 3,066
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A C E G [auth H] I [auth J] A, C, E, G [auth H], I [auth J], K [auth L]	329	Influenza A virus (A/duck/Laos/3295/2006(H5N1))	Mutation(s): 0 Gene Names: HA, hemagglutinin
UniProt
Find proteins for Q00G25 (Influenza A virus) Explore Q00G25 Go to UniProtKB: Q00G25
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00G25
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B D F H [auth I] J [auth K] B, D, F, H [auth I], J [auth K], L [auth M]	182	Influenza A virus (A/duck/Laos/3295/2006(H5N1))	Mutation(s): 0 Gene Names: HA, hemagglutinin
UniProt
Find proteins for Q00G25 (Influenza A virus) Explore Q00G25 Go to UniProtKB: Q00G25
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00G25
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth G], N, O, P	2		N-Glycosylation	Interactions Focus chain M [auth G] Focus chain N Focus chain O Focus chain P Interactions & Density Focus chain M [auth G] Focus chain N Focus chain O Focus chain P
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth E] SDF format, chain U [auth H] SDF format, chain V [auth J] SDF format, chain W [auth J] SDF format, chain X [auth L] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth E] MOL2 format, chain U [auth H] MOL2 format, chain V [auth J] MOL2 format, chain W [auth J] MOL2 format, chain X [auth L]	Q [auth A] R [auth C] S [auth C] T [auth E] U [auth H] Q [auth A], R [auth C], S [auth C], T [auth E], U [auth H], V [auth J], W [auth J], X [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth E] Focus chain U [auth H] Focus chain V [auth J] Focus chain W [auth J] Focus chain X [auth L] Interactions & Density Focus chain Q [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth E] Focus chain U [auth H] Focus chain V [auth J] Focus chain W [auth J] Focus chain X [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.254
R-Value Work: 0.196
R-Value Observed: 0.199
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.584	α = 83.94
b = 71.557	β = 85.46
c = 247.054	γ = 60.68

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-05-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-07
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

4JUL

Crystal structure of H5N1 influenza virus hemagglutinin, clade 2.3.4

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2