9B7H | pdb_00009b7h

Crystal structure of the H3 hemagglutinin COBRA TJ2

PDB DOI: https://doi.org/10.2210/pdb9B7H/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-03-27 Released: 2025-05-07
Deposition Author(s): Dzimianski, J.V., DuBois, R.M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free:
0.269 (Depositor), 0.270 (DCC)
R-Value Work:
0.222 (Depositor), 0.222 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Assessing the structural boundaries of broadly reactive antibody interactions with diverse H3 influenza hemagglutinin proteins

Dzimianski, J.V., Nagashima, K.A., Cruz, J.M., Sautto, G.A., O'Rourke, S.M., Serrao, V.B.H., Ross, T.M., Mousa, J.J., DuBois, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 183.08 kDa
Atom Count: 12,439
Modeled Residue Count: 1,470
Deposited Residue Count: 1,515
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, B, C	323	Influenza A virus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A Focus chain B Focus chain C
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	D [auth a], E [auth b], F [auth c]	182	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0FCI1 (Influenza A virus) Explore A0FCI1 Go to UniProtKB: A0FCI1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0FCI1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D [auth a] Focus chain F [auth c]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth E], H [auth D], I [auth F], K [auth H], M [auth J], G [auth E], H [auth D], I [auth F], K [auth H], M [auth J], P [auth M], R [auth O]	5		N-Glycosylation	Interactions Focus chain G [auth E] Focus chain H [auth D] Focus chain I [auth F] Focus chain K [auth H] Focus chain M [auth J] Focus chain P [auth M] Focus chain R [auth O] Interactions & Density Focus chain G [auth E] Focus chain H [auth D] Focus chain I [auth F] Focus chain K [auth H] Focus chain M [auth J] Focus chain P [auth M] Focus chain R [auth O]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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	J [auth G], N [auth K], T [auth Q], U [auth R]	2		N-Glycosylation	Interactions Focus chain J [auth G] Focus chain N [auth K] Focus chain T [auth Q] Focus chain U [auth R] Interactions & Density Focus chain J [auth G] Focus chain N [auth K] Focus chain T [auth Q] Focus chain U [auth R]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
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	L [auth I], O [auth L], S [auth P]	3		N-Glycosylation	Interactions Focus chain L [auth I] Focus chain O [auth L] Focus chain S [auth P] Interactions & Density Focus chain L [auth I] Focus chain O [auth L] Focus chain S [auth P]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
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	Q [auth N]	4		N-Glycosylation	Interactions Focus chain Q [auth N] Interactions & Density Focus chain Q [auth N]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain DA [auth a] SDF format, chain FA [auth c] SDF format, chain W [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain CA [auth C] SDF format, chain V [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth a] MOL2 format, chain FA [auth c] MOL2 format, chain W [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain V [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain DA [auth a] mmCIF format, chain FA [auth c] mmCIF format, chain W [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain V [auth A]	AA [auth C] BA [auth C] CA [auth C] DA [auth a] FA [auth c] AA [auth C], BA [auth C], CA [auth C], DA [auth a], FA [auth c], V [auth A], W [auth A], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth a] Focus chain FA [auth c] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth a] Focus chain FA [auth c] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth b] MOL2 format, chain EA [auth b] mmCIF format, chain EA [auth b]	EA [auth b]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth b] Interactions & Density Focus chain EA [auth b]