SMTL ID : 8t51.1 (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-2-1-mer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: Y.62, K.67, G.68, R.69, F.70, T.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.68 SO4.2: 2 residues within 4Å: Chain A: K.54, Y.58 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.58, A:Y.58 Water bridges: A:K.54 Salt bridges: A:K.54 SO4.3: 4 residues within 4Å: Chain A: S.113, A.115, F.147, G.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.113 Water bridges: A:G.175 SO4.10: 2 residues within 4Å: Chain B: R.27, S.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.28 Water bridges: B:R.27 SO4.11: 4 residues within 4Å: Chain B: G.16, E.17, P.18 Ligands: ACT.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.17 SO4.20: 2 residues within 4Å: Chain C: G.135, T.136 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.136, C:T.136

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 2 residues within 4Å: Chain A: E.64 Chain B: D.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.64, B:D.1, B:D.1 ZN.7: 3 residues within 4Å: Chain A: H.165 Chain B: N.142 Chain C: E.1 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:H.165, C:E.1, H2O.2, H2O.10, H2O.13 ZN.9: 2 residues within 4Å: Chain A: E.1 Chain C: H.165 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:H.165, A:E.1, H2O.1, H2O.4, H2O.11 ZN.16: 2 residues within 4Å: Chain B: D.156, H.194 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.156, B:H.194, H2O.9 ZN.19: 2 residues within 4Å: Chain B: D.190, H.194 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.190, B:H.194, H2O.9, H2O.9

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: D.56, N.57, Y.58, A.59, T.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.57, A:T.60 Water bridges: A:T.60 GOL.8: 8 residues within 4Å: Chain A: V.164, H.165, T.166 Chain B: T.169, E.170, Q.171, D.172, T.177 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:E.170, B:T.177, A:V.164, A:T.166 GOL.12: 13 residues within 4Å: Chain A: F.167, P.168, A.169, V.170, S.178, L.179, S.180 Chain B: Q.165, E.166, S.167, S.181, S.182, T.183 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.167, B:T.183, B:T.183, A:S.178, A:S.178, A:S.180 GOL.13: 8 residues within 4Å: Chain B: L.42, K.44, Q.50, P.64, R.66, F.67, E.86, D.87 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.44, B:Q.50, B:E.86 GOL.21: 5 residues within 4Å: Chain C: D.56, N.57, Y.58, A.59, T.60 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.57, C:Y.58, C:T.60 Water bridges: C:T.60 GOL.22: 6 residues within 4Å: Chain C: Y.62, K.67, G.68, R.69, F.70, T.71 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.68, C:F.70

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

ACT.6: 5 residues within 4Å: Chain A: V.2, Q.3, L.4, W.104 Chain C: S.162 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:L.4, C:S.162 ACT.17: 3 residues within 4Å: Chain B: G.16, R.82 Ligands: SO4.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.82 ACT.18: 4 residues within 4Å: Chain B: R.147, A.149, E.166, V.168 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.147, B:V.168 Hydrogen bonds: B:R.147, B:A.149, B:E.166 ACT.23: 6 residues within 4Å: Chain C: F.167, P.168, V.170, S.178, L.179, S.180 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.170 Hydrogen bonds: C:S.178, C:S.180

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

PEG.14: 10 residues within 4Å: Chain A: G.42, K.43, G.44 Chain B: L.9, V.90, Y.92, P.105, G.106, T.107, K.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.92, B:P.105, B:P.105 PEG.15: 5 residues within 4Å: Chain B: V.115, A.116, A.117, Q.204, G.205 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.115, B:A.117, B:G.205

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 heavy chain: AC
3.10C2 Fab light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

3.10C2 Fab heavy chain

3.10C2 Fab light chain

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