5Y2M | pdb_00005y2m

Crystal structure of a group 2 HA binding antibody AF4H1K1 Fab in complex with the H4N6 duck isolate (H4-CZ/56) hemagglutinin

PDB DOI: https://doi.org/10.2210/pdb5Y2M/pdb

Classification: IMMUNE SYSTEM
Organism(s): Influenza A virus (A/duck/Czechoslovakia/1956(H4N6)), Homo sapiens
Expression System: Trichoplusia ni, Homo sapiens
Mutation(s): No

Deposited: 2017-07-26 Released: 2019-02-13
Deposition Author(s): Xiao, H., Qi, J., Gao, F.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free:
0.277 (Depositor), 0.281 (DCC)
R-Value Work:
0.235 (Depositor), 0.243 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

An H3-clade neutralizing antibody screened from an H7N9 patient that binds group 2 influenza A hemagglutinins

Xiao, H., Qi, J., Gao, F.G.

To be published.

Macromolecule Content

Total Structure Weight: 268.7 kDa
Atom Count: 18,315
Modeled Residue Count: 2,345
Deposited Residue Count: 2,415
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C [auth B], E [auth C]	327	Influenza A virus (A/duck/Czechoslovakia/1956(H4N6))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A3KF09 (Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6)) Explore A3KF09 Go to UniProtKB: A3KF09
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3KF09
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C [auth B] Focus chain E [auth C]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B [auth D], D [auth E], F	176	Influenza A virus (A/duck/Czechoslovakia/1956(H4N6))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A3KF09 (Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6)) Explore A3KF09 Go to UniProtKB: A3KF09
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3KF09
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
a group 2 HA binding antibody AF4H1K1 Fab heavy chain	G [auth I], I [auth K]	233	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
a group 2 HA binding antibody AF4H1K1 Fab light chain	H [auth J], J [auth L]	220	Homo sapiens	Mutation(s): 0

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free: 0.277 (Depositor), 0.281 (DCC)
R-Value Work: 0.235 (Depositor), 0.243 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.175	α = 90
b = 140.94	β = 95.31
c = 138.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-02-13

Deposition Author(s):

Xiao, H.

Qi, J.

Gao, F.G.

Revision History (Full details and data files)

Version 1.0: 2019-02-13
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-11-20
Changes: Structure summary