6ID3

Crystal structure of H7 hemagglutinin mutant H7-SGPL ( A138S, V186G) from the influenza virus A/Anhui/1/2013 (H7N9)

PDB DOI: https://doi.org/10.2210/pdb6ID3/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2018-09-08 Released: 2019-11-27
Deposition Author(s): Gao, G.F., Xu, Y., Qi, J.X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.275
R-Value Work: 0.248
R-Value Observed: 0.249

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 56.07 kDa
Atom Count: 3,824
Modelled Residue Count: 475
Deposited Residue Count: 498
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 chain	A	321	Influenza A virus	Mutation(s): 2 Gene Names: HA
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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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B	177	Influenza A virus	Mutation(s): 0 Gene Names: HA
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

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 C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B]	C [auth A], D [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.275
R-Value Work: 0.248
R-Value Observed: 0.249
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.629	α = 90
b = 115.629	β = 90
c = 294.096	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Gao, G.F.

Xu, Y.

Qi, J.X.

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 1.1: 2019-12-04
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary

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6ID3

Crystal structure of H7 hemagglutinin mutant H7-SGPL ( A138S, V186G) from the influenza virus A/Anhui/1/2013 (H7N9)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2