4LKG

The structure of hemagglutinin from a avian-origin H7N9 influenza virus (A/Shanghai/1/2013) in complex with avian receptor analog 3'SLNLN

PDB DOI: https://doi.org/10.2210/pdb4LKG/pdb

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

Deposited: 2013-07-07 Released: 2013-11-06
Deposition Author(s): Shi, Y., Zhang, W., Wang, F., Qi, J., Song, H., Wu, Y., Gao, F., Zhang, Y., Fan, Z., Gong, W., Wang, D., Shu, Y., Wang, Y., Yan, J., Gao, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free: 0.278
R-Value Work: 0.246
R-Value Observed: 0.247

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: 164.64 kDa
Atom Count: 11,531
Modelled Residue Count: 1,458
Deposited Residue Count: 1,458
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	316	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for V5IRV0 (Influenza A virus) Explore V5IRV0 Go to UniProtKB: V5IRV0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V5IRV0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
hemagglutinin	B, D, F	170	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for V5IRU7 (Influenza A virus) Explore V5IRU7 Go to UniProtKB: V5IRU7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V5IRU7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
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	G	3		N/A	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G00065MO GlyCosmos: G00065MO GlyGen: G00065MO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose	H, I	2		N/A	Interactions Focus chain H Focus chain I Interactions & Density Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G30207PZ GlyCosmos: G30207PZ GlyGen: G30207PZ

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 L [auth F] SDF format, chain J [auth B] SDF format, chain K [auth D] MOL2 format, chain L [auth F] MOL2 format, chain J [auth B] MOL2 format, chain K [auth D]	J [auth B], K [auth D], L [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth F] Interactions & Density Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth F]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067 Query on PRD_900067	G	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog		Interactions Focus chain G Interactions & Density Focus chain G

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free: 0.278
R-Value Work: 0.246
R-Value Observed: 0.247
Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.764	α = 90
b = 110.764	β = 90
c = 133.227	γ = 120

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: 2013-11-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-06
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary