4QY1

Structure of H10 from human-infecting H10N8 in complex with avian receptor

PDB DOI: https://doi.org/10.2210/pdb4QY1/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2014-07-23 Released: 2015-01-28
Deposition Author(s): Wang, M., Zhang, W., Qi, J., Wang, F., Zhou, J., Bi, Y., Wu, Y., Sun, H., Liu, J., Huang, C., Li, X., Yan, J., Shu, Y., Shi, Y., Gao, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.246
R-Value Work: 0.197
R-Value Observed: 0.200

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: 666.47 kDa
Atom Count: 48,138
Modelled Residue Count: 5,904
Deposited Residue Count: 5,904
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	A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	318	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for A0A059T4A1 (Influenza A virus) Explore A0A059T4A1 Go to UniProtKB: A0A059T4A1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A059T4A1
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	B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	174	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for A0A059T4A1 (Influenza A virus) Explore A0A059T4A1 Go to UniProtKB: A0A059T4A1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A059T4A1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Y	2		N-Glycosylation	Interactions Focus chain Y Interactions & Density Focus chain Y
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], Z	3		N/A	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain Z
Glycosylation Resources
GlyTouCan: G00065MO GlyCosmos: G00065MO GlyGen: G00065MO

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 AB [auth W] SDF format, chain BB [auth X] SDF format, chain DA [auth A] SDF format, chain EA [auth B] SDF format, chain FA [auth C] SDF format, chain GA [auth D] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain JA [auth F] SDF format, chain KA [auth G] SDF format, chain LA [auth H] SDF format, chain MA [auth I] SDF format, chain NA [auth J] SDF format, chain OA [auth K] SDF format, chain PA [auth L] SDF format, chain QA [auth M] SDF format, chain RA [auth N] SDF format, chain SA [auth O] SDF format, chain TA [auth P] SDF format, chain UA [auth Q] SDF format, chain VA [auth R] SDF format, chain WA [auth S] SDF format, chain XA [auth T] SDF format, chain YA [auth U] SDF format, chain ZA [auth V] MOL2 format, chain AB [auth W] MOL2 format, chain BB [auth X] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain MA [auth I] MOL2 format, chain NA [auth J] MOL2 format, chain OA [auth K] MOL2 format, chain PA [auth L] MOL2 format, chain QA [auth M] MOL2 format, chain RA [auth N] MOL2 format, chain SA [auth O] MOL2 format, chain TA [auth P] MOL2 format, chain UA [auth Q] MOL2 format, chain VA [auth R] MOL2 format, chain WA [auth S] MOL2 format, chain XA [auth T] MOL2 format, chain YA [auth U] MOL2 format, chain ZA [auth V]	AB [auth W] BB [auth X] DA [auth A] EA [auth B] FA [auth C] AB [auth W], BB [auth X], DA [auth A], EA [auth B], FA [auth C], GA [auth D], HA [auth E], IA [auth E], JA [auth F], KA [auth G], LA [auth H], MA [auth I], NA [auth J], OA [auth K], PA [auth L], QA [auth M], RA [auth N], SA [auth O], TA [auth P], UA [auth Q], VA [auth R], WA [auth S], XA [auth T], YA [auth U], ZA [auth V]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth W] Focus chain BB [auth X] Focus chain DA [auth A] Focus chain EA [auth B] Focus chain FA [auth C] Focus chain GA [auth D] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain JA [auth F] Focus chain KA [auth G] Focus chain LA [auth H] Focus chain MA [auth I] Focus chain NA [auth J] Focus chain OA [auth K] Focus chain PA [auth L] Focus chain QA [auth M] Focus chain RA [auth N] Focus chain SA [auth O] Focus chain TA [auth P] Focus chain UA [auth Q] Focus chain VA [auth R] Focus chain WA [auth S] Focus chain XA [auth T] Focus chain YA [auth U] Focus chain ZA [auth V] Interactions & Density Focus chain AB [auth W] Focus chain BB [auth X] Focus chain DA [auth A] Focus chain EA [auth B] Focus chain FA [auth C] Focus chain GA [auth D] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain JA [auth F] Focus chain KA [auth G] Focus chain LA [auth H] Focus chain MA [auth I] Focus chain NA [auth J] Focus chain OA [auth K] Focus chain PA [auth L] Focus chain QA [auth M] Focus chain RA [auth N] Focus chain SA [auth O] Focus chain TA [auth P] Focus chain UA [auth Q] Focus chain VA [auth R] Focus chain WA [auth S] Focus chain XA [auth T] Focus chain YA [auth U] Focus chain ZA [auth V]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067 Query on PRD_900067	AA [auth Z], BA [auth a], CA [auth b], Z [auth c]	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog		Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain Z

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.246
R-Value Work: 0.197
R-Value Observed: 0.200
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.257	α = 94.96
b = 111.439	β = 101.17
c = 222.346	γ = 91.9

Software Package:

Software Name	Purpose
ADSC	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: 2015-01-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-01-28
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: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary