4N5Z

Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D, N224K, Q226L and T318I) from the influenza virus A/Viet Nam/1203/2004 (H5N1)

PDB DOI: https://doi.org/10.2210/pdb4N5Z/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2013-10-10 Released: 2013-11-20
Deposition Author(s): Zhu, X., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.281
R-Value Work: 0.233
R-Value Observed: 0.235

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: 895.89 kDa
Atom Count: 60,979
Modelled Residue Count: 7,515
Deposited Residue Count: 7,725
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 chain	A B [auth C] C [auth E] D [auth G] E [auth I] A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K], G [auth M], H [auth O], I [auth Q], J [auth S], K [auth U], L [auth W], M [auth Y], N [auth a], O [auth c]	334	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 4 Gene Names: HA
UniProt
Find proteins for Q5EP31 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q5EP31 Go to UniProtKB: Q5EP31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5EP31
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	AA [auth X] BA [auth Z] CA [auth b] DA [auth d] P [auth B] AA [auth X], BA [auth Z], CA [auth b], DA [auth d], P [auth B], Q [auth D], R [auth F], S [auth H], T [auth J], U [auth L], V [auth N], W [auth P], X [auth R], Y [auth T], Z [auth V]	181	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q6DQ33 Go to UniProtKB: Q6DQ33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6DQ33
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
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	EA [auth e], GA [auth g], HA [auth h], JA [auth j], LA [auth l], EA [auth e], GA [auth g], HA [auth h], JA [auth j], LA [auth l], NA [auth n], OA [auth o], PA [auth p], RA [auth r], TA [auth t], VA [auth v], XA [auth x]	3		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain RA [auth r] Focus chain TA [auth t] Focus chain VA [auth v] Focus chain XA [auth x] Interactions & Density Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain RA [auth r] Focus chain TA [auth t] Focus chain VA [auth v] Focus chain XA [auth x]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AB [auth 0], FA [auth f], IA [auth i], KA [auth k], MA [auth m], AB [auth 0], FA [auth f], IA [auth i], KA [auth k], MA [auth m], QA [auth q], SA [auth s], UA [auth u], WA [auth w], YA [auth y], ZA [auth z]	2		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain QA [auth q] Focus chain SA [auth s] Focus chain UA [auth u] Focus chain WA [auth w] Focus chain YA [auth y] Focus chain ZA [auth z] Interactions & Density Focus chain AB [auth 0] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain QA [auth q] Focus chain SA [auth s] Focus chain UA [auth u] Focus chain WA [auth w] Focus chain YA [auth y] Focus chain ZA [auth z]
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 BB [auth C] SDF format, chain CB [auth K] SDF format, chain DB [auth M] SDF format, chain EB [auth O] SDF format, chain FB [auth Y] SDF format, chain GB [auth a] SDF format, chain HB [auth c] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth K] MOL2 format, chain DB [auth M] MOL2 format, chain EB [auth O] MOL2 format, chain FB [auth Y] MOL2 format, chain GB [auth a] MOL2 format, chain HB [auth c]	BB [auth C] CB [auth K] DB [auth M] EB [auth O] FB [auth Y] BB [auth C], CB [auth K], DB [auth M], EB [auth O], FB [auth Y], GB [auth a], HB [auth c]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BB [auth C] Focus chain CB [auth K] Focus chain DB [auth M] Focus chain EB [auth O] Focus chain FB [auth Y] Focus chain GB [auth a] Focus chain HB [auth c] Interactions & Density Focus chain BB [auth C] Focus chain CB [auth K] Focus chain DB [auth M] Focus chain EB [auth O] Focus chain FB [auth Y] Focus chain GB [auth a] Focus chain HB [auth c]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.281
R-Value Work: 0.233
R-Value Observed: 0.235
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.24	α = 88.43
b = 118.943	β = 89.68
c = 273.41	γ = 60.26

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-11-20

Deposition Author(s):

Zhu, X.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2013-11-20
Type: Initial release
Version 1.1: 2014-01-01
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: 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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4N5Z

Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D, N224K, Q226L and T318I) from the influenza virus A/Viet Nam/1203/2004 (H5N1)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2