SMTL ID : 8s6z.3 (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-2-2-2-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain C: N.19, Y.80 No protein-ligand interaction detected (PLIP)

7 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 3 residues within 4Å: Chain A: P.41, E.151 Ligands: ZN.5 No protein-ligand interaction detected (PLIP) IMD.8: 3 residues within 4Å: Chain B: D.9, Q.106 Ligands: ZN.12 No protein-ligand interaction detected (PLIP) IMD.9: 3 residues within 4Å: Chain B: K.189, E.193 Ligands: ZN.17 No protein-ligand interaction detected (PLIP) IMD.23: 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 IMD.26: 4 residues within 4Å: Chain D: P.41, L.111, E.151 Ligands: ZN.29 No protein-ligand interaction detected (PLIP) IMD.31: 3 residues within 4Å: Chain E: S.188, D.191 Ligands: ZN.35 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.188 IMD.48: 3 residues within 4Å: Chain D: S.30 Chain F: K.2, D.106 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.2, F:K.2

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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.7: 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 A, 3 interactions with chain B Hydrogen bonds: A:P.170, A:S.180, A:S.182, B:S.168, B:T.184, B:T.184 GOL.20: 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 GOL.27: 3 residues within 4Å: Chain D: G.56, T.58 Chain F: Y.51 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.58 GOL.28: 11 residues within 4Å: Chain D: F.169, P.170, V.172, S.180, L.181, S.182 Chain E: Q.166, E.167, S.168, S.182, T.184 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:E.167, E:S.168, E:S.182, D:S.182, D:S.182 GOL.32: 5 residues within 4Å: Chain B: L.15, G.16, E.17 Chain E: R.60, V.64 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:R.60, E:V.64, B:E.17

26 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.5: 3 residues within 4Å: Chain A: E.151, A.171 Ligands: IMD.2 No protein-ligand interaction detected (PLIP) ZN.6: 1 residues within 4Å: Chain A: E.46 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.46 ZN.10: 5 residues within 4Å: Chain A: H.167, T.186 Chain B: N.143, N.144 Chain D: E.1 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Metal complexes: D:E.1, D:E.1, A:H.167 ZN.11: 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.12: 2 residues within 4Å: Chain B: D.9 Ligands: IMD.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.9 ZN.13: 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.14: 3 residues within 4Å: Chain A: H.167 Chain B: D.173 Chain D: E.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.173, B:D.173 ZN.15: 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.16: 3 residues within 4Å: Chain B: D.66 Chain E: S.83, Q.85 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B Metal complexes: E:S.83, B:D.66 ZN.17: 3 residues within 4Å: Chain B: K.189, E.193 Ligands: IMD.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.193 ZN.24: 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.25: 2 residues within 4Å: Chain C: H.116, V.117 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.116 ZN.29: 3 residues within 4Å: Chain D: E.151, A.171 Ligands: IMD.26 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.151 ZN.30: 2 residues within 4Å: Chain D: D.62 Chain E: D.1 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.62 ZN.33: 2 residues within 4Å: Chain E: D.157, H.195 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.157, E:H.195 ZN.34: 5 residues within 4Å: Chain A: E.1 Chain D: H.167, T.186 Chain E: N.143, N.144 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Metal complexes: D:H.167, A:E.1, A:E.1 ZN.35: 3 residues within 4Å: Chain E: S.188, D.191 Ligands: IMD.31 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.191 ZN.36: 2 residues within 4Å: Chain E: E.61, S.62 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.61, E:E.61, H2O.1 ZN.37: 3 residues within 4Å: Chain E: Q.85, A.86, E.87 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.87, E:E.87 ZN.38: 1 residues within 4Å: Chain E: D.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.9 ZN.39: 3 residues within 4Å: Chain D: K.132 Chain E: N.216, E.219 No protein-ligand interaction detected (PLIP) ZN.40: 3 residues within 4Å: Chain A: E.1 Chain D: H.167 Chain E: D.173 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.173, E:D.173 ZN.41: 1 residues within 4Å: Chain E: E.167 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.167 ZN.42: 2 residues within 4Å: Chain E: K.155, E.201 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.201, E:E.201 ZN.49: 5 residues within 4Å: Chain F: R.34, S.36, H.38, E.46, K.95 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.38, F:E.46

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

NAG.18: 1 residues within 4Å: Chain C: N.87 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.87 NAG.19: 2 residues within 4Å: Chain C: V.5, N.111 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.111 NAG.21: 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.22: 4 residues within 4Å: Chain C: N.27, F.29, N.74, E.75 No protein-ligand interaction detected (PLIP) NAG.43: 2 residues within 4Å: Chain F: N.19, Y.80 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.19, F:Y.80 NAG.44: 3 residues within 4Å: Chain F: Y.85, V.86, N.87 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.87 NAG.45: 1 residues within 4Å: Chain F: N.111 No protein-ligand interaction detected (PLIP) NAG.46: 2 residues within 4Å: Chain F: N.53, Q.57 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Q.57 Hydrogen bonds: F:Q.57 NAG.47: 3 residues within 4Å: Chain F: N.27, N.74, E.75 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.27, F: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: AD
Light chain of AI3 antibody: BE
T-cell-specific surface glycoprotein CD28: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Heavy chain Fab fragment of AI3 antibody

Light chain of AI3 antibody

T-cell-specific surface glycoprotein CD28

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