SMTL ID : 8s6z.1 (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

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 3 residues within 4Å: Chain A: P.41, E.151 Ligands: ZN.4 No protein-ligand interaction detected (PLIP) IMD.7: 3 residues within 4Å: Chain B: D.9, Q.106 Ligands: ZN.11 No protein-ligand interaction detected (PLIP) IMD.8: 3 residues within 4Å: Chain B: K.189, E.193 Ligands: ZN.16 No protein-ligand interaction detected (PLIP) IMD.22: 3 residues within 4Å: Chain A: S.30 Chain C: K.2, D.106 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: 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 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.51, A:T.58 GOL.6: 9 residues within 4Å: Chain A: L.144, F.169, P.170, S.180, L.181, S.182 Chain B: S.168, S.182, T.184 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.168, B:T.184, B:T.184, A:P.170, A:S.180, A:S.182 GOL.19: 4 residues within 4Å: Chain C: G.40, L.41, D.42, D.90 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.41

13 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: D.62 Chain B: D.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.62, H2O.1, H2O.1 ZN.4: 3 residues within 4Å: Chain A: E.151, A.171 Ligands: IMD.1 No protein-ligand interaction detected (PLIP) ZN.5: 1 residues within 4Å: Chain A: E.46 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.46 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 A: D.104 Chain B: E.61, S.62 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.61, B:E.61, H2O.1, H2O.1, H2O.1 ZN.11: 2 residues within 4Å: Chain B: D.9 Ligands: IMD.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.9 ZN.12: 2 residues within 4Å: Chain B: K.194, H.195 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.195, H2O.1 ZN.13: 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.14: 2 residues within 4Å: Chain B: Q.85, E.87 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.87, B:E.87 ZN.15: 1 residues within 4Å: Chain B: D.66 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.66 ZN.16: 3 residues within 4Å: Chain B: K.189, E.193 Ligands: IMD.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.193 ZN.23: 2 residues within 4Å: Chain C: H.38, E.46 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.38, C:E.46 ZN.24: 2 residues within 4Å: Chain C: H.116, V.117 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.116

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

NAG.17: 1 residues within 4Å: Chain C: N.87 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.87 NAG.18: 2 residues within 4Å: Chain C: V.5, N.111 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.111 NAG.20: 3 residues within 4Å: Chain C: N.53, Q.57, Q.59 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.57 NAG.21: 4 residues within 4Å: Chain C: N.27, F.29, N.74, E.75 No protein-ligand interaction detected (PLIP)

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
A

B
B

C
C

Heavy chain Fab fragment of AI3 antibody

Light chain of AI3 antibody

T-cell-specific surface glycoprotein CD28

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