4N5Y

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

PDB DOI: https://doi.org/10.2210/pdb4N5Y/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: 3.16 Å
R-Value Free: 0.262
R-Value Work: 0.213
R-Value Observed: 0.215

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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 895.69 kDa
Atom Count: 60,964
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): 3 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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	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], QA [auth q], WA [auth w], YA [auth y]	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 QA [auth q] Focus chain WA [auth w] Focus chain YA [auth y] 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 QA [auth q] Focus chain WA [auth w] Focus chain YA [auth y]
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], BB [auth 1], FA [auth f], IA [auth i], KA [auth k], AB [auth 0], BB [auth 1], FA [auth f], IA [auth i], KA [auth k], MA [auth m], PA [auth p], RA [auth r], TA [auth t], UA [auth u], VA [auth v], XA [auth x], ZA [auth z]	2		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain BB [auth 1] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain PA [auth p] Focus chain RA [auth r] Focus chain TA [auth t] Focus chain UA [auth u] Focus chain VA [auth v] Focus chain XA [auth x] Focus chain ZA [auth z] Interactions & Density Focus chain AB [auth 0] Focus chain BB [auth 1] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain PA [auth p] Focus chain RA [auth r] Focus chain TA [auth t] Focus chain UA [auth u] Focus chain VA [auth v] Focus chain XA [auth x] Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	SA [auth s]	4		N-Glycosylation	Interactions Focus chain SA [auth s] Interactions & Density Focus chain SA [auth s]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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 CB [auth K] SDF format, chain DB [auth O] SDF format, chain EB [auth Y] SDF format, chain FB [auth c] SDF format, chain GB [auth c] MOL2 format, chain CB [auth K] MOL2 format, chain DB [auth O] MOL2 format, chain EB [auth Y] MOL2 format, chain FB [auth c] MOL2 format, chain GB [auth c]	CB [auth K], DB [auth O], EB [auth Y], FB [auth c], GB [auth c]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CB [auth K] Focus chain DB [auth O] Focus chain EB [auth Y] Focus chain FB [auth c] Focus chain GB [auth c] Interactions & Density Focus chain CB [auth K] Focus chain DB [auth O] Focus chain EB [auth Y] Focus chain FB [auth c] Focus chain GB [auth c]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.16 Å
R-Value Free: 0.262
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.915	α = 91.5
b = 118.105	β = 90.18
c = 273.799	γ = 119.87

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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Help and Resources

4N5Y

Crystal structure of H5 hemagglutinin mutant (N158D, N224K and Q226L) 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

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)