SMTL ID : 5jds.1

Crystal structure of PD-L1 complexed with a nanobody at 1.7 Angstron resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-oligomer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: N.75, N.76 Ligands: CL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.76 Water bridges: A:A.77 NA.6: 2 residues within 4Å: Chain B: L.32, S.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.32

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

CL.2: 3 residues within 4Å: Chain A: Y.61, A.63, D.64 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: R.49, V.50, A.51, Y.61, A.63 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: N.75, N.76 Ligands: NA.1 Ligand excluded by PLIP

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

SO4.5: 3 residues within 4Å: Chain A: Q.118 Chain B: Y.107, R.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.107, B:Y.107 Salt bridges: B:R.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, F. et al., Structural basis of a novel PD-L1 nanobody for immune checkpoint blockade. Cell Discov (2017)

Release Date

2017-04-12

Peptides

Nanobody: A
Programmed cell death 1 ligand 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Nanobody

Programmed cell death 1 ligand 1