SMTL ID : 9pwn.1

Crystal structure of Fabs 7411 in complex with TREM2 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: R.19, S.71, Y.80, Q.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.19, A:R.19, A:S.71

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: A.24, S.25, G.26, F.27, N.77 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.24, A:G.26, A:F.27 GOL.3: 1 residues within 4Å: Chain A: K.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.76 GOL.4: 5 residues within 4Å: Chain A: G.199, T.200, Q.201, T.202, E.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.200, A:E.221

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: Q.180, S.181 Chain B: Q.160, T.180 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.181, A:S.181, B:Q.160, B:T.180 SO4.6: 3 residues within 4Å: Chain A: L.11, S.124, T.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.125, A:T.125 SO4.7: 2 residues within 4Å: Chain A: T.58, Y.60 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.58, A:T.58, A:Y.60 Water bridges: A:T.58 SO4.8: 5 residues within 4Å: Chain A: S.170, G.171, H.173, T.192 Chain B: N.138 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.138, B:D.170, A:G.171 Water bridges: B:N.137, B:N.137 SO4.9: 3 residues within 4Å: Chain A: F.27, T.28, R.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.28 Water bridges: A:R.32 Salt bridges: A:R.32 SO4.11: 4 residues within 4Å: Chain B: Q.37, K.39, K.42, K.45 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.39, B:K.42, B:K.45 SO4.12: 5 residues within 4Å: Chain B: P.113, S.114, V.115, V.205, K.207 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.115 Salt bridges: B:K.207 SO4.13: 4 residues within 4Å: Chain B: G.200, L.201, S.202, S.203 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.202, B:S.202, B:S.203

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

EDO.10: 2 residues within 4Å: Chain A: Q.3, L.5 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain B: D.1, Q.3, S.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.26, B:S.26 EDO.15: 3 residues within 4Å: Chain B: P.8, S.9, S.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.9, B:S.10, B:S.10 EDO.16: 3 residues within 4Å: Chain B: R.18, V.19, T.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

da Silva Almeida, A. et al., Building a potent TREM2 agonistic, biparatopic, common light chain antibody. Mabs (2025)

Release Date

2025-09-10

Peptides

7411 Fab Heavy Chain: A
7411 Fab Light Chain: B
TREM-2 stalk peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

7411 Fab Heavy Chain

7411 Fab Light Chain

TREM-2 stalk peptide