7TTZ | pdb_00007ttz

Heterodimeric IgA Fc in complex with Staphylococcus aureus protein SSL7

PDB DOI: https://doi.org/10.2210/pdb7TTZ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Staphylococcus aureus
Expression System: Homo sapiens, Escherichia coli
Mutation(s): Yes

Deposited: 2022-02-02 Released: 2023-02-01
Deposition Author(s): Boulanger, M.J., Verstraete, M., Heinkel, F., Escobar, E., Dixit, S., Von Kreudenstein, T.S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.247 (Depositor), 0.250 (DCC)
R-Value Work:
0.200 (Depositor), 0.204 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Engineering a pure and stable heterodimeric IgA for the development of multispecific therapeutics.

Heinkel, F., Verstraete, M.M., Cao, S., Li, J., Farber, P., Stangle, E., Silva-Moreno, B., Peng, F., Dixit, S., Boulanger, M.J., Spreter Von Kreudenstein, T., Escobar-Cabrera, E.

(2022) MAbs 14: 2141637-2141637

PubMed: 36343329 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1080/19420862.2022.2141637
Primary Citation Related Structures:
7TTZ

PubMed Abstract:
CE-SDS: capillary electrophoresis sodium dodecyl sulfate; DSC: differential scanning calorimetry; FACS: fluorescence-activated cell sorting; FSA: full-sized antibody; Her2: human epidermal growth factor receptor 2; MFI: mean fluorescent intensity; OAA: one-armed antibody; PBS: phosphate-buffered saline; PDB: Protein Data Bank; SEC: size-exclusion chromatography; prepSEC (preparative SEC); RMSD: root-mean-square deviation; RU: resonance units; SPR: surface plasmon resonance; TAA: tumor-associated antigen; WT: wild-type.

Organizational Affiliation

Zymeworks Inc., Vancouver, BC, Canada.

Macromolecule Content

Total Structure Weight: 96.21 kDa
Atom Count: 6,512
Modeled Residue Count: 795
Deposited Residue Count: 842
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IgA Fc	A	220	Homo sapiens	Mutation(s): 6
UniProt
Find proteins for Q6MZV6 (Homo sapiens) Explore Q6MZV6 Go to UniProtKB: Q6MZV6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6MZV6
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IgA Fc	B	220	Homo sapiens	Mutation(s): 7
UniProt
Find proteins for Q6MZV6 (Homo sapiens) Explore Q6MZV6 Go to UniProtKB: Q6MZV6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6MZV6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Superantigen-like protein SSL7	C, D	201	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for A0A9Y2YA69 (Staphylococcus aureus) Explore A0A9Y2YA69 Go to UniProtKB: A0A9Y2YA69
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9Y2YA69
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PG (Subject of Investigation/LOI) Query on 1PG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D]	F [auth A] G [auth A] H [auth A] J [auth B] K [auth B] F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], N [auth C], P [auth D]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C₁₁ H₂₄ O₆ SLNYBUIEAMRFSZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D]
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C]	I [auth A], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth C] Interactions & Density Focus chain I [auth A] Focus chain O [auth C]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	L [auth B], M [auth B], Q [auth D], R [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth D] Focus chain R [auth D]