SMTL ID : 8rpb.1

Structure of S79 Fab in complex with IgV domain of human PD-L1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: E.46, W.47 Chain B: V.101, F.102 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: V.2, Q.3, L.4, Y.105, W.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.4, A:L.4, A:Q.108 GOL.3: 5 residues within 4Å: Chain A: S.7, G.8, T.110, K.204 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.8, A:T.110 GOL.4: 5 residues within 4Å: Chain A: G.109, T.110, L.111, P.152 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.110, A:L.111

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: S.52, S.54, G.56, S.57 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.52, A:S.54, A:G.56, A:S.57, A:S.57 Water bridges: A:G.53, A:S.54 SO4.6: 1 residues within 4Å: Chain A: R.19 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.19 SO4.7: 3 residues within 4Å: Chain B: S.61, R.63, Q.81 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.61, B:Q.81 Salt bridges: B:R.63 SO4.8: 4 residues within 4Å: Chain A: Q.39 Chain B: Q.40, G.43, K.44 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.43, A:Q.39 SO4.9: 6 residues within 4Å: Chain A: G.42, K.43, G.44 Chain B: D.87, Y.89, G.104 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.87 SO4.10: 2 residues within 4Å: Chain C: K.108, R.109 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.109, C:R.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malinge, P. et al., Structural analysis of light chain-driven bispecific antibodies targeting CD47 and PD-L1. Mabs (2024)

Release Date

2024-06-19

Peptides

heavy chain of S79 fab: A
light chain of S79 fab: B
Programmed cell death 1 ligand 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
P

heavy chain of S79 fab

light chain of S79 fab

Programmed cell death 1 ligand 1

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