SMTL ID : 8t51.2 (1 other biounit)

Crystal structure of Fab 3.10C2 bound to TREM2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-2-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: D.172, D.175 Ligands: GOL.3 No protein-ligand interaction detected (PLIP) SO4.2: 4 residues within 4Å: Chain A: I.35, Y.54, R.55, N.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.58 Salt bridges: A:R.55

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: T.169, E.170, Q.171, D.172, T.177 Ligands: SO4.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.172 Water bridges: A:E.170 GOL.4: 6 residues within 4Å: Chain A: L.30, T.36, M.56, G.71, S.72, G.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.36, A:T.36, A:G.73 Water bridges: A:T.36 GOL.6: 9 residues within 4Å: Chain A: L.42, K.44, Q.50, I.63, P.64, R.66, F.67, E.86, D.87 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.44, A:E.86, A:E.86 Water bridges: A:Q.50, A:Q.50

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 3 residues within 4Å: Chain A: R.113, N.143, D.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.143 Salt bridges: A:R.113

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

PEG.7: 3 residues within 4Å: Chain B: V.8, S.11, S.13 No protein-ligand interaction detected (PLIP) PEG.11: 6 residues within 4Å: Chain A: Y.39, L.51, Y.54 Chain C: V.8, S.11, S.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.11, C:S.13

3 x ZN: ZINC ION(Non-covalent)

ZN.8: 1 residues within 4Å: Chain B: H.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.10 ZN.9: 1 residues within 4Å: Chain C: E.18 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.18, C:E.18, H2O.6 ZN.10: 1 residues within 4Å: Chain C: H.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsiao, Y.C. et al., Rapid affinity optimization of an anti-TREM2 clinical lead antibody by cross-lineage immune repertoire mining. Nat Commun (2024)

Release Date

2024-06-19

Peptides

3.10C2 Fab light chain: A
Triggering receptor expressed on myeloid cells 2 peptide: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

3.10C2 Fab light chain

Triggering receptor expressed on myeloid cells 2 peptide

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