SMTL ID : 8f0l.1

Crystal Structure of the Human T cell Receptor CD3(EPSILON) N-Terminal Peptide Complexed with ADI-26906 FAB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

hetero-2-2-2-mer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 13 residues within 4Å: Chain A: F.172, P.173, A.174, V.175, S.183, L.184, S.185 Chain B: Q.165, E.166, S.167, S.181, S.182, T.183 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:F.172, A:S.183, A:S.185, B:S.167, B:S.181, B:T.183 Water bridges: A:S.183 GOL.2: 5 residues within 4Å: Chain A: F.27, N.28, D.31, Y.32, R.98 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.28, A:N.28, A:D.31, A:Y.32, A:Y.32 Water bridges: A:R.98 GOL.3: 4 residues within 4Å: Chain A: N.161, S.162, A.164, I.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.161 GOL.4: 9 residues within 4Å: Chain B: Q.43, K.45, K.51, L.53, P.65, R.67, F.68, E.87, D.88 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.43, B:Q.43, B:Q.43, B:K.51, B:D.88 Water bridges: B:K.45, B:R.67 GOL.5: 10 residues within 4Å: Chain A: Q.177, S.178 Chain B: G.162, N.163, S.164, Q.165, T.185 Chain C: A.62, K.63, Q.65 8 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:S.164, B:T.185, C:A.62, A:S.178 Water bridges: B:N.163, B:Q.165, B:T.185, A:S.179 GOL.6: 13 residues within 4Å: Chain C: F.172, P.173, A.174, V.175, S.183, L.184, S.185 Chain D: Q.165, E.166, S.167, S.181, S.182, T.183 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.165, D:S.167, D:T.183, C:P.173, C:S.183, C:S.185 GOL.7: 10 residues within 4Å: Chain D: Q.43, K.45, K.51, L.53, V.64, P.65, R.67, F.68, E.87, D.88 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.43, D:Q.43, D:K.51, D:R.67, D:E.87, D:D.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C.Y. et al., Structure-based engineering of a novel CD3 epsilon-targeting antibody for reduced polyreactivity. Mabs (2023)

Release Date

2023-03-29

Peptides

ADI-26906 Fab Heavy Chain: AC
ADI-26906 Fab Light Chain: BD
T-cell surface glycoprotein CD3 epsilon chain: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

C
A

B
L

D
B

E
P

F
Q

ADI-26906 Fab Heavy Chain

ADI-26906 Fab Light Chain

T-cell surface glycoprotein CD3 epsilon chain