6P6P

Crystal structure of hemagglutinin from influenza virus A/Sichuan/2/1987 (H3N2)

PDB DOI: https://doi.org/10.2210/pdb6P6P/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Sichuan/2/1987(H3N2))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2019-06-04 Released: 2020-07-01
Deposition Author(s): Dai, Y.N., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.251
R-Value Work: 0.221
R-Value Observed: 0.230

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of hemagglutinin from influenza virus A/Sichuan/2/1987 (H3N2)

Dai, Y.N., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 343.74 kDa
Atom Count: 24,621
Modelled Residue Count: 2,931
Deposited Residue Count: 2,982
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B, C, D, E A, B, C, D, E, F	497	Influenza A virus (A/Sichuan/2/1987(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for H9XCU1 (Influenza A virus) Explore H9XCU1 Go to UniProtKB: H9XCU1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H9XCU1
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain 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
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, J, K G, H, I, J, K, L	3		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain JA [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 A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain JA [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 A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain JA [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 A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth E] DA [auth E] EA [auth E] AA [auth D], BA [auth D], CA [auth E], DA [auth E], EA [auth E], FA [auth E], GA [auth F], HA [auth F], IA [auth F], JA [auth F], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth D], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.251
R-Value Work: 0.221
R-Value Observed: 0.230
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.94	α = 90
b = 149.94	β = 135.01
c = 150.09	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Coot	model building
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Dai, Y.N.

Fremont, D.H.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2020-07-01
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary