SMTL ID : 8aok.1

Complex of PD-L1 with VHH6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 3 residues within 4Å: Chain A: K.88, Q.90 Ligands: OXM.3 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.88, A:Q.90, A:Q.90, A:Q.90 PEG.4: 4 residues within 4Å: Chain A: V.51, H.52 Chain B: L.103, S.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.52 PEG.9: 3 residues within 4Å: Chain B: S.18, Q.83, N.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.18, B:Q.83, B:N.85

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 1 residues within 4Å: Chain A: L.71 No protein-ligand interaction detected (PLIP)

1 x OXM: OXAMIC ACID(Non-covalent)

OXM.3: 5 residues within 4Å: Chain A: Y.15, K.88, L.89, Q.90 Ligands: PEG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.15, A:L.89, A:Q.90, A:Q.90

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 3 residues within 4Å: Chain A: E.55, R.69, K.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.55, A:R.69, A:R.69 EDO.6: 5 residues within 4Å: Chain A: K.29, D.32, A.35, Y.101, G.102 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.35, A:G.102

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 3 residues within 4Å: Chain A: F.2, T.3, D.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.2

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 10 residues within 4Å: Chain A: D.44 Chain B: F.48, Y.60, Y.61, T.62, D.63, K.66, Y.104, R.109, T.110 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.109, B:R.109, A:D.44 Water bridges: B:F.48, B:Y.60, B:T.62, B:D.63, B:Y.104, B:R.109, B:R.109, B:T.110, B:T.110, B:T.110, B:T.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang-Pettinger, T. et al., Identification, binding, and structural characterization of single domain anti-PD-L1 antibodies inhibitory of immune regulatory proteins PD-1 and CD80. J.Biol.Chem. (2023)

Release Date

2023-06-14

Peptides

Programmed cell death 1 ligand 1: A
VHH 6: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Programmed cell death 1 ligand 1

VHH 6