SMTL ID : 8s6z.2 (2 other biounits)

CD28 in complex with the antibody Fab fragment AI3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 4 residues within 4Å: Chain A: P.41, L.111, E.151 Ligands: ZN.4 No protein-ligand interaction detected (PLIP) IMD.6: 3 residues within 4Å: Chain B: S.188, D.191 Ligands: ZN.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.188 IMD.23: 3 residues within 4Å: Chain A: S.30 Chain C: K.2, D.106 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.2, C:K.2

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: G.56, T.58 Chain C: Y.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.58 GOL.3: 11 residues within 4Å: Chain A: F.169, P.170, V.172, S.180, L.181, S.182 Chain B: Q.166, E.167, S.168, S.182, T.184 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.167, B:S.168, B:S.182, A:S.182, A:S.182 GOL.7: 2 residues within 4Å: Chain B: R.60, V.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.60, B:V.64

13 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain A: E.151, A.171 Ligands: IMD.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.151 ZN.5: 2 residues within 4Å: Chain A: D.62 Chain B: D.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.62 ZN.8: 2 residues within 4Å: Chain B: D.157, H.195 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.157, B:H.195 ZN.9: 4 residues within 4Å: Chain A: H.167, T.186 Chain B: N.143, N.144 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.167 ZN.10: 3 residues within 4Å: Chain B: S.188, D.191 Ligands: IMD.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.191 ZN.11: 2 residues within 4Å: Chain B: E.61, S.62 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.61, B:E.61, H2O.1 ZN.12: 3 residues within 4Å: Chain B: Q.85, A.86, E.87 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.87, B:E.87 ZN.13: 1 residues within 4Å: Chain B: D.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.9 ZN.14: 3 residues within 4Å: Chain A: K.132 Chain B: N.216, E.219 No protein-ligand interaction detected (PLIP) ZN.15: 2 residues within 4Å: Chain A: H.167 Chain B: D.173 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.173, B:D.173 ZN.16: 1 residues within 4Å: Chain B: E.167 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.167 ZN.17: 2 residues within 4Å: Chain B: K.155, E.201 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.201, B:E.201 ZN.24: 5 residues within 4Å: Chain C: R.34, S.36, H.38, E.46, K.95 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.38, C:E.46

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.18: 2 residues within 4Å: Chain C: N.19, Y.80 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.19, C:Y.80 NAG.19: 3 residues within 4Å: Chain C: Y.85, V.86, N.87 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.87 NAG.20: 1 residues within 4Å: Chain C: N.111 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain C: N.53, Q.57 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Q.57 Hydrogen bonds: C:Q.57 NAG.22: 3 residues within 4Å: Chain C: N.27, N.74, E.75 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.27, C:N.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Majocchi, S. et al., NI-3201 is a bispecific antibody mediating PD-L1-dependent CD28 costimulation on T cells for enhanced tumor control. Cancer Immunology Research (2024)

Release Date

2024-12-18

Peptides

Heavy chain Fab fragment of AI3 antibody: A
Light chain of AI3 antibody: B
T-cell-specific surface glycoprotein CD28: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Heavy chain Fab fragment of AI3 antibody

Light chain of AI3 antibody

T-cell-specific surface glycoprotein CD28

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