8X27 | pdb_00008x27

Crystal structure of H5 hemagglutinin from human-infecting H5N8 influenza virus in complex with LSTc

PDB DOI: https://doi.org/10.2210/pdb8X27/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Influenza A virus
Expression System: Baculovirus transfer vector pFASTBAC1
Mutation(s): No

Deposited: 2023-11-09 Released: 2025-05-14
Deposition Author(s): Jin, X.Y., Han, P., Song, H., Qi, J.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free:
0.242 (Depositor), 0.242 (DCC)
R-Value Work:
0.211 (Depositor), 0.211 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Enhanced binding of Sialyl Lewis X to hemagglutinin contributes to H5N8 mammalian pathogenicity and infectivity

Jin, X., Han, P., Zhang, C., Maio, A.D., Shi, Y., Qi, J., Bi, Y., Liu, Y., Song, H., Gao, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 353.07 kDa
Atom Count: 23,757
Modeled Residue Count: 2,909
Deposited Residue Count: 3,036
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A B [auth C] C [auth D] D [auth B] E A, B [auth C], C [auth D], D [auth B], E, F	506	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A8E4ZAK5 (Influenza A virus) Explore A0A8E4ZAK5 Go to UniProtKB: A0A8E4ZAK5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8E4ZAK5
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B [auth C] Focus chain C [auth D] Focus chain E Focus chain F
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, J	3		N/A	Interactions Focus chain G Focus chain J Interactions & Density Focus chain G Focus chain J
Glycosylation Resources
GlyTouCan: G73578JC GlyCosmos: G73578JC GlyGen: G73578JC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose	H, I	4		N/A	Interactions Focus chain H Focus chain I Interactions & Density Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G03509EL GlyCosmos: G03509EL GlyGen: G03509EL

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose	K	4		N/A	Interactions Focus chain K Interactions & Density Focus chain K

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L	2		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
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 R [auth C] SDF format, chain S [auth D] SDF format, chain U [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain X [auth F] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain X [auth F] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E] mmCIF format, chain X [auth F] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	M [auth A] N [auth A] O [auth A] P [auth C] Q [auth C] M [auth A], N [auth A], O [auth A], P [auth C], Q [auth C], R [auth C], S [auth D], T [auth D], U [auth D], V [auth E], W [auth E], X [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth F] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth F]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900046 Query on PRD_900046	G, J	6'-sialyl-N-acetyllactosamine	Oligosaccharide / Glycan component		Interactions Focus chain G Focus chain J Interactions & Density Focus chain G Focus chain J