8S6Z

CD28 in complex with the antibody Fab fragment AI3

PDB DOI: https://doi.org/10.2210/pdb8S6Z/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens, Cricetulus griseus
Mutation(s): No

Deposited: 2024-02-28 Released: 2024-12-18
Deposition Author(s): Majocchi, S., Giovanni, M., Malinge, P., Fischer, N., Svensson, L.A., Kelpsas, V., Rose, N.C.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.258
R-Value Work: 0.198

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

NI-3201 is a bispecific antibody mediating PD-L1-dependent CD28 costimulation on T cells for enhanced tumor control

Majocchi, S., Giovanni, M., Malinge, P., Fischer, N., Svensson, L.A., Kelpsas, V.

(2024) Cancer Immunology Research

DOI: https://doi.org/10.1158/2326-6066.CIR-24-0298

Macromolecule Content

Total Structure Weight: 130.83 kDa
Atom Count: 8,785
Modelled Residue Count: 1,110
Deposited Residue Count: 1,154
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain Fab fragment of AI3 antibody	A, D	223	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of AI3 antibody	B, E	220	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell-specific surface glycoprotein CD28	C, F	134	Homo sapiens	Mutation(s): 0 Gene Names: CD28
UniProt & NIH Common Fund Data Resources
Find proteins for P10747 (Homo sapiens) Explore P10747 Go to UniProtKB: P10747
PHAROS: P10747 GTEx: ENSG00000178562
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10747
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain C Focus chain F	Go to GlyGen: P10747-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth F] SDF format, chain BA [auth C] SDF format, chain WA [auth F] SDF format, chain X [auth C] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain YA [auth F] SDF format, chain ZA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain WA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth F] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain WA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth F] mmCIF format, chain ZA [auth F]	AA [auth C] AB [auth F] BA [auth C] WA [auth F] X [auth C] AA [auth C], AB [auth F], BA [auth C], WA [auth F], X [auth C], XA [auth F], Y [auth C], YA [auth F], ZA [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain WA [auth F] Focus chain X [auth C] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain WA [auth F] Focus chain X [auth C] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain ZA [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain LA [auth E] SDF format, chain M [auth B] SDF format, chain Z [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth B] mmCIF format, chain Z [auth C]	GA [auth D] HA [auth D] I [auth A] LA [auth E] M [auth B] GA [auth D], HA [auth D], I [auth A], LA [auth E], M [auth B], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain LA [auth E] Focus chain M [auth B] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain LA [auth E] Focus chain M [auth B] Focus chain Z [auth C]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain CA [auth C] SDF format, chain FA [auth D] SDF format, chain H [auth A] SDF format, chain KA [auth E] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain BB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain BB [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	BB [auth F] CA [auth C] FA [auth D] H [auth A] KA [auth E] BB [auth F], CA [auth C], FA [auth D], H [auth A], KA [auth E], N [auth B], O [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain BB [auth F] Focus chain CA [auth C] Focus chain FA [auth D] Focus chain H [auth A] Focus chain KA [auth E] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain BB [auth F] Focus chain CA [auth C] Focus chain FA [auth D] Focus chain H [auth A] Focus chain KA [auth E] Focus chain N [auth B] Focus chain O [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain CB [auth F] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain P [auth B] SDF format, chain PA [auth E] SDF format, chain Q [auth B] SDF format, chain QA [auth E] SDF format, chain R [auth B] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain SA [auth E] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain W [auth B] MOL2 format, chain CB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain W [auth B] mmCIF format, chain CB [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain OA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain W [auth B]	CB [auth F] DA [auth C] EA [auth C] IA [auth D] J [auth A] CB [auth F], DA [auth C], EA [auth C], IA [auth D], J [auth A], JA [auth D], K [auth A], L [auth A], MA [auth E], NA [auth E], OA [auth E], P [auth B], PA [auth E], Q [auth B], QA [auth E], R [auth B], RA [auth E], S [auth B], SA [auth E], T [auth B], TA [auth E], U [auth B], UA [auth E], V [auth B], VA [auth E], W [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CB [auth F] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth B] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Interactions & Density Focus chain CB [auth F] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth B] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B]