SMTL ID : 9q8l.1

Crystal Structure of 21A08Ap1-Fab in Complex with Human PD-1 at 1.85 angstrom Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-1-mer

Ligands

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.1: 6 residues within 4Å: Chain A: S.54, F.56 Chain C: D.25, N.26, V.88, R.89 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.89, C:R.89 NAG-NAG-FUC.2: 10 residues within 4Å: Chain C: N.35, T.36, S.37, E.38, F.40, F.59, P.60, Q.76, L.77, G.80 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.40, C:F.59 Hydrogen bonds: C:E.38, C:E.38, C:Q.76

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

EDO.3: 6 residues within 4Å: Chain A: Y.101, D.103 Chain B: Y.50 Chain C: S.15, P.16, A.17 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Y.101, A:D.103, C:A.17 Water bridges: C:F.14, C:F.14 EDO.4: 8 residues within 4Å: Chain A: K.145, V.171, Q.173, S.179 Chain B: T.135, E.164, Y.181, S.183 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:E.164, B:S.183 Hydrogen bonds: A:S.179 EDO.5: 5 residues within 4Å: Chain A: S.54, G.55, R.72, D.73, N.74 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.54, A:D.73, A:D.73, A:N.74 Water bridges: A:R.72 EDO.8: 6 residues within 4Å: Chain B: S.118, V.119, T.120, L.139, I.140, S.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.118, B:T.120, B:T.120, B:S.141

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 3 residues within 4Å: Chain A: N.157, A.160, Q.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.157

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 6 residues within 4Å: Chain A: K.43, G.44 Chain B: D.86, Y.88, G.103, G.104 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.86, B:Y.88

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

NAG.9: 2 residues within 4Å: Chain C: R.91, N.93 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.92, C:R.92, C:N.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murer, P. et al., ANV600 is a novel PD-1 targeted IL-2R beta gamma agonist that selectively expands tumor antigen-specific T cells and potentiates PD-1 checkpoint inhibitor therapy. J Immunother Cancer (2025)

Release Date

2025-08-13

Peptides

Heavy chain of huIgG1-Fab: A
Light chain of huIgG1-Fab: B
Programmed cell death protein 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

Heavy chain of huIgG1-Fab

Light chain of huIgG1-Fab

Programmed cell death protein 1