4DJ6

Structure of the hemagglutinin from a highly pathogenic H7N7 influenza virus

PDB DOI: https://doi.org/10.2210/pdb4DJ6/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Netherlands/219/2003(H7N7))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2012-02-01 Released: 2012-06-20
Deposition Author(s): Yang, H., Carney, P.J., Donis, R.O., Stevens, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.236
R-Value Work: 0.203
R-Value Observed: 0.205

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: 171.79 kDa
Atom Count: 11,804
Modelled Residue Count: 1,459
Deposited Residue Count: 1,512
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C, E	327	Influenza A virus (A/Netherlands/219/2003(H7N7))	Mutation(s): 0
UniProt
Find proteins for Q6VMK1 (Influenza A virus) Explore Q6VMK1 Go to UniProtKB: Q6VMK1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6VMK1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, D, F	177	Influenza A virus (A/Netherlands/219/2003(H7N7))	Mutation(s): 0
UniProt
Find proteins for Q6VMK1 (Influenza A virus) Explore Q6VMK1 Go to UniProtKB: Q6VMK1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6VMK1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	G	2		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
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 H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain R [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F]	H [auth A] I [auth A] J [auth B] K [auth C] L [auth C] H [auth A], I [auth A], J [auth B], K [auth C], L [auth C], M [auth C], N [auth D], O [auth E], P [auth E], Q [auth E], R [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.236
R-Value Work: 0.203
R-Value Observed: 0.205
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.949	α = 90
b = 116.573	β = 124.92
c = 117.32	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-06-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-20
Type: Initial release
Version 1.1: 2013-01-02
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

4DJ6

Structure of the hemagglutinin from a highly pathogenic H7N7 influenza virus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2