SMTL ID : 7vux.1

Complex structure of PD1 and 609A-Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x THR: THREONINE(Covalent)

THR.1: 2 residues within 4Å: Chain A: V.121, P.122 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: T.1 Water bridges: T.1

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: S.30, E.31, S.32, F.33, F.52, P.53 Ligands: GOL.7 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.30, A:F.33 Water bridges: A:S.32, B:G.53 GOL.3: 3 residues within 4Å: Chain A: T.15, D.18, R.117 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.18, A:R.117, A:R.117 Water bridges: A:T.15, A:D.18, A:D.18 GOL.6: 6 residues within 4Å: Chain B: V.167, H.168 Chain C: T.164, E.165, Q.166, D.167 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Q.166, B:V.167, B:T.169 Water bridges: C:E.165, C:S.168, C:T.172, B:H.168 GOL.7: 10 residues within 4Å: Chain A: S.32, F.33, P.53 Chain B: S.31, Y.32, D.33, P.99, Y.100, G.101 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.31, B:D.33, B:P.99, B:G.101 GOL.12: 6 residues within 4Å: Chain B: Q.39 Chain C: Q.38, K.39, P.40, G.41, Q.42 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.41, C:Q.42, C:Q.42 GOL.16: 6 residues within 4Å: Chain A: N.36, Y.38, K.48 Chain C: K.49, Y.50, Q.53 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:K.48, A:K.48, C:K.49, C:Q.53 Water bridges: A:N.36 GOL.17: 3 residues within 4Å: Chain C: K.149, N.152, A.193 5 PLIP interactions: 5 interactions with chain C Water bridges: C:K.149, C:K.149, C:N.152, C:E.195, C:E.195

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

EDO.4: 3 residues within 4Å: Chain A: Q.69, L.70, P.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.69, A:P.71 EDO.8: 6 residues within 4Å: Chain B: E.152, P.153, V.154, P.171, A.172, L.182 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.149, B:V.154, B:V.154, B:A.172 EDO.9: 4 residues within 4Å: Chain B: P.130, S.132, S.134, T.135 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.131, B:S.132, B:T.135 EDO.10: 11 residues within 4Å: Chain B: F.170, P.171, A.172, V.173, S.181, L.182, S.183 Chain C: S.162, S.176 Ligands: EDO.11, MG.18 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:P.171, B:V.173, B:S.183, C:S.162, C:S.176 Water bridges: B:S.183 EDO.11: 7 residues within 4Å: Chain B: L.145, V.173, S.181, L.182 Chain C: T.178 Ligands: EDO.10, MG.18 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.181, B:S.181, C:T.178 EDO.14: 3 residues within 4Å: Chain A: A.99 Chain B: Y.59 Chain C: W.94 No protein-ligand interaction detected (PLIP) EDO.15: 3 residues within 4Å: Chain C: L.125, Y.186, R.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.211

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: S.57 Chain B: D.105 Chain C: L.46 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.105, H2O.7, H2O.25 MG.18: 8 residues within 4Å: Chain C: Q.160, E.161, S.162, S.176, S.177, T.178 Ligands: EDO.10, EDO.11 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Q.160, C:S.176, C:T.178, H2O.18

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

PEG.13: 4 residues within 4Å: Chain C: V.110, A.111, A.112, G.200 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.112

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

CL.19: 1 residues within 4Å: Chain C: E.81 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, J. et al., A strategy for the efficient construction of anti-PD1-based bispecific antibodies with desired IgG-like properties. Mabs (2022)

Release Date

2021-11-17

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Programmed cell death protein 1

Heavy chain of Fab fragment

Light chain of Fab fragment