8Q6K

Human IgD Fab in complex with an orthosteric inhibitor of Phl p 7

PDB DOI: https://doi.org/10.2210/pdb8Q6K/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Camelidae mixed library
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2023-08-11 Released: 2023-12-06
Deposition Author(s): Davies, A.M., Vester, S.K., McDonnell, J.M.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.259
R-Value Work: 0.214
R-Value Observed: 0.216

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Expanding the Anti-Phl p 7 Antibody Toolkit: An Anti-Idiotype Nanobody Inhibitor.

Vester, S.K., Davies, A.M., Beavil, R.L., Sandhar, B.S., Beavil, A.J., Gould, H.J., Sutton, B.J., McDonnell, J.M.

(2023) Antibodies (Basel) 12

PubMed: 37987253 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.3390/antib12040075
Primary Citation of Related Structures:
8Q6K

PubMed Abstract:
We have previously produced a toolkit of antibodies, comprising recombinant human antibodies of all but one of the human isotypes, directed against the polcalcin family antigen Phl p 7. In this work, we complete the toolkit of human antibody isotypes with the IgD version of the anti-Phl p 7 monoclonal antibody. We also raised a set of nanobodies against the IgD anti-Phl p 7 antibody and identify and characterize one paratope-specific nanobody. This nanobody also binds to the IgE isotype of this antibody, which shares the same idiotype, and orthosterically inhibits the interaction with Phl p 7. The 2.1 Å resolution X-ray crystal structure of the nanobody in complex with the IgD Fab is described.

Organizational Affiliation

Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, London SE1 1UL, UK.

Macromolecule Content

Total Structure Weight: 64.94 kDa
Atom Count: 4,478
Modelled Residue Count: 570
Deposited Residue Count: 591
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human IgD Fab light chain	A [auth L]	217	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human IgD Fab heavy chain	B [auth H]	227	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 072	C [auth N]	147	Camelidae mixed library	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth L] SDF format, chain E [auth H] SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain P [auth N] MOL2 format, chain D [auth L] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain P [auth N] mmCIF format, chain D [auth L] mmCIF format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain P [auth N]	D [auth L] E [auth H] F [auth H] G [auth H] H D [auth L], E [auth H], F [auth H], G [auth H], H, I [auth H], J [auth H], K [auth H], L [auth H], P [auth N]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain P [auth N] Interactions & Density Focus chain D [auth L] Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain P [auth N]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain M [auth H] SDF format, chain N [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H] mmCIF format, chain M [auth H] mmCIF format, chain N [auth H]	M [auth H], N [auth H]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth H] Focus chain N [auth H] Interactions & Density Focus chain M [auth H] Focus chain N [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth H] MOL2 format, chain O [auth H] mmCIF format, chain O [auth H]	O [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth H] Interactions & Density Focus chain O [auth H]