7S11

Crystal structure of Fab in complex with mouse CD96 monomer

PDB DOI: https://doi.org/10.2210/pdb7S11/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Rattus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-08-31 Released: 2021-11-03
Deposition Author(s): Lee, P.S., Chau, B., Strop, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.279
R-Value Work: 0.226
R-Value Observed: 0.228

Starting Models: 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

Antibody blockade of CD96 by distinct molecular mechanisms.

Lee, P.S., Chau, B., Barman, I., Bee, C., Jashnani, A., Hogan, J.M., Aguilar, B., Dollinger, G., Rajpal, A., Strop, P.

(2021) MAbs 13: 1979800-1979800

PubMed: 34595996 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1080/19420862.2021.1979800
Primary Citation of Related Structures:
7S11, 7S13

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

Total Structure Weight: 246.73 kDa
Atom Count: 16,283
Modelled Residue Count: 2,141
Deposited Residue Count: 2,268
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface protein tactile	A [auth C], D, G [auth E], J [auth F]	122	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 A [auth C] Focus chain D	Go to GlyGen: Q3U0X8-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	B [auth H], E [auth I], H [auth J], K	229	Rattus	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
Fab light chain	C [auth L], F [auth M], I [auth N], L [auth O]	216	Rattus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	M [auth C], P [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain M [auth C] Focus chain P [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain O [auth L] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth N] SDF format, chain T [auth K] MOL2 format, chain N [auth C] MOL2 format, chain O [auth L] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth N] MOL2 format, chain T [auth K] mmCIF format, chain N [auth C] mmCIF format, chain O [auth L] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth N] mmCIF format, chain T [auth K]	N [auth C] O [auth L] Q [auth D] R [auth D] S [auth N] N [auth C], O [auth L], Q [auth D], R [auth D], S [auth N], T [auth K]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain N [auth C] Focus chain O [auth L] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth N] Focus chain T [auth K] Interactions & Density Focus chain N [auth C] Focus chain O [auth L] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth N] Focus chain T [auth K]