SMTL ID : 7cu5.1

N-Glycosylation of PD-1 and glycosylation dependent binding of PD-1 specific monoclonal antibody camrelizumab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

hetero-2-2-mer

Ligands

1 x NAG- NAG- MAN- MAN- FUC: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN-FUC.1: 9 residues within 4Å: Chain A: N.29, T.30, S.31, E.32, F.34, F.53, Q.70, P.72, G.74 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.34, A:F.53 Hydrogen bonds: A:Q.70

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 5 residues within 4Å: Chain A: N.20, T.69, S.80, R.83 Chain C: S.129 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.69 Hydrogen bonds: A:R.83 NAG-NAG-FUC.6: 4 residues within 4Å: Chain D: N.20, R.67, T.69, R.83 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:R.67, D:T.69 Hydrogen bonds: D:R.83

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

NAG.3: 2 residues within 4Å: Chain A: M.41, N.45 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: R.85, N.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.87 NAG.7: 1 residues within 4Å: Chain D: N.87 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.87

1 x NAG- NAG- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN-FUC.5: 8 residues within 4Å: Chain D: N.29, T.30, S.31, E.32, F.34, F.53, Q.70, G.74 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.53 Hydrogen bonds: D:Q.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, K. et al., N-glycosylation of PD-1 promotes binding of camrelizumab. Embo Rep. (2020)

Release Date

2020-10-14

Peptides

Programmed cell death protein 1: AD
camrelizumab-scFv: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

D
E

B
B

C
A

Programmed cell death protein 1

camrelizumab-scFv