SMTL ID : 6jjp.2 (1 other biounit)

Crystal structure of Fab of a PD-1 monoclonal antibody MW11-h317 in complex with PD-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-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-BMA-MAN-FUC.1: 15 residues within 4Å: Chain A: S.31, G.53, G.54, S.56, Y.57, R.72, N.74 Chain C: N.38, T.39, S.40, E.41, F.43, F.62, Q.79, G.83 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:G.54, A:N.74, A:S.31, A:G.53, A:G.54, C:Q.79, A:R.72, A:N.74, A:S.56 Hydrophobic interactions: C:F.43, C:F.62

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

NAG.2: 3 residues within 4Å: Chain C: N.29, R.76, V.91 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.76 NAG.3: 1 residues within 4Å: Chain C: N.96 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.94, C:N.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, M. et al., Identification of a monoclonal antibody that targets PD-1 in a manner requiring PD-1 Asn58 glycosylation. Commun Biol (2019)

Release Date

2019-10-30

Peptides

Heavy chain of MW11-h317: A
light chain of MW11-h317: B
Programmed cell death protein 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Heavy chain of MW11-h317

light chain of MW11-h317

Programmed cell death protein 1

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