4LN8

The crystal structure of hemagglutinin from a h7n9 influenza virus (a/shanghai/2/2013) in complex with lstb

PDB DOI: https://doi.org/10.2210/pdb4LN8/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Shanghai/02/2013(H7N9))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2013-07-11 Released: 2013-10-02
Deposition Author(s): Yang, H., Carney, P.J., Chang, J.C., Villanueva, J.M., Stevens, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.246
R-Value Work: 0.217
R-Value Observed: 0.219

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 348.97 kDa
Atom Count: 23,845
Modelled Residue Count: 2,898
Deposited Residue Count: 3,036
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	325	Influenza A virus (A/Shanghai/02/2013(H7N9))	Mutation(s): 0
UniProt
Find proteins for R4NN21 (Influenza A virus) Explore R4NN21 Go to UniProtKB: R4NN21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	R4NN21
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, D, F, H, J B, D, F, H, J, L	181	Influenza A virus (A/Shanghai/02/2013(H7N9))	Mutation(s): 0
UniProt
Find proteins for R4NN21 (Influenza A virus) Explore R4NN21 Go to UniProtKB: R4NN21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	R4NN21
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	M, P, S	4		N-Glycosylation	Interactions Focus chain M Focus chain P Focus chain S Interactions & Density Focus chain M Focus chain P Focus chain S
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 4
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	N, Q, T, V, X N, Q, T, V, X, Z	3		N-Glycosylation	Interactions Focus chain N Focus chain Q Focus chain T Focus chain V Focus chain X Focus chain Z Interactions & Density Focus chain N Focus chain Q Focus chain T Focus chain V Focus chain X Focus chain Z
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose	AA [auth a], O, W	4		N/A	Interactions Focus chain AA [auth a] Focus chain O Focus chain W Interactions & Density Focus chain AA [auth a] Focus chain O Focus chain W
Glycosylation Resources
GlyTouCan: G91415NU GlyCosmos: G91415NU GlyGen: G91415NU

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	R, Y	3		N/A	Interactions Focus chain R Focus chain Y Interactions & Density Focus chain R Focus chain Y
Glycosylation Resources
GlyTouCan: G66658UG GlyCosmos: G66658UG GlyGen: G66658UG

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	U	2		N/A	Interactions Focus chain U Interactions & Density Focus chain U
Glycosylation Resources
GlyTouCan: G07539OP GlyCosmos: G07539OP GlyGen: G07539OP

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 EA [auth D] SDF format, chain GA [auth F] SDF format, chain IA [auth H] SDF format, chain MA [auth L] SDF format, chain CA [auth B] SDF format, chain KA [auth J] MOL2 format, chain EA [auth D] MOL2 format, chain GA [auth F] MOL2 format, chain IA [auth H] MOL2 format, chain MA [auth L] MOL2 format, chain CA [auth B] MOL2 format, chain KA [auth J]	CA [auth B] EA [auth D] GA [auth F] IA [auth H] KA [auth J] CA [auth B], EA [auth D], GA [auth F], IA [auth H], KA [auth J], MA [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth B] Focus chain EA [auth D] Focus chain GA [auth F] Focus chain IA [auth H] Focus chain KA [auth J] Focus chain MA [auth L] Interactions & Density Focus chain CA [auth B] Focus chain EA [auth D] Focus chain GA [auth F] Focus chain IA [auth H] Focus chain KA [auth J] Focus chain MA [auth L]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain DA [auth C] SDF format, chain FA [auth E] SDF format, chain HA [auth G] SDF format, chain JA [auth I] SDF format, chain LA [auth K] MOL2 format, chain BA [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth E] MOL2 format, chain HA [auth G] MOL2 format, chain JA [auth I] MOL2 format, chain LA [auth K]	BA [auth A] DA [auth C] FA [auth E] HA [auth G] JA [auth I] BA [auth A], DA [auth C], FA [auth E], HA [auth G], JA [auth I], LA [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain DA [auth C] Focus chain FA [auth E] Focus chain HA [auth G] Focus chain JA [auth I] Focus chain LA [auth K] Interactions & Density Focus chain BA [auth A] Focus chain DA [auth C] Focus chain FA [auth E] Focus chain HA [auth G] Focus chain JA [auth I] Focus chain LA [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.246
R-Value Work: 0.217
R-Value Observed: 0.219
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.361	α = 90
b = 154.441	β = 90
c = 154.061	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	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: 2013-10-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-02
Type: Initial release
Version 1.1: 2013-10-30
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary

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4LN8

The crystal structure of hemagglutinin from a h7n9 influenza virus (a/shanghai/2/2013) in complex with lstb

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)