7S13

Experimental Data Snapshot

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

(2021) MAbs 13: 1979800-1979800

PubMed Abstract:
The molecular interactions of mouse CD96 to CD155 ligand and to two surrogate antibodies have been investigated. Biophysical and structural studies demonstrate that CD96 forms a homodimer but assembles as 1:1 heterodimeric complexes with CD155 or with one of the surrogate antibodies, which compete for the same binding interface. In comparison, the other surrogate antibody binds across the mouse CD96 dimer and recognizes a quaternary epitope spanning both protomers to block exposure of the ligand-binding site. This study reveals different blocking mechanisms and modalities of these two antibodies and may provide insight into the functional effects of antibodies against CD96.

Organizational Affiliation

Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, CA, USA.

Macromolecule Content

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	A [auth H], C [auth I]	226	Rattus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	B [auth L], D [auth M]	213	Rattus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface protein tactile	E [auth C], F [auth D]	125	Mus musculus	Mutation(s): 0 Gene Names: Cd96
UniProt & NIH Common Fund Data Resources
Find proteins for Q3U0X8 (Mus musculus) Explore Q3U0X8 Go to UniProtKB: Q3U0X8
IMPC: MGI:1934368
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3U0X8
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E [auth C] Focus chain F [auth D]	Go to GlyGen: Q3U0X8-1
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Reference Sequence

Small Molecules

Ligands 3 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 C] SDF format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	K [auth C], L [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain K [auth C] Focus chain L [auth D]
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain J [auth I] MOL2 format, chain J [auth I] mmCIF format, chain J [auth I]	J [auth I]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain J [auth I] Interactions & Density Focus chain J [auth I]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain H [auth L] SDF format, chain I [auth L] MOL2 format, chain G [auth H] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] mmCIF format, chain G [auth H] mmCIF format, chain H [auth L] mmCIF format, chain I [auth L]	G [auth H], H [auth L], I [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Focus chain H [auth L] Focus chain I [auth L] Interactions & Density Focus chain G [auth H] Focus chain H [auth L] Focus chain I [auth L]