SMTL ID : 8t59.1 (1 other biounit)

Crystal structure of Para.09 bound to TREM2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: V.2, Q.3, L.4, Y.104, W.105 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.4, A:L.4, A:W.105 Water bridges: A:W.105 GOL.2: 6 residues within 4Å: Chain A: A.40, S.41, T.93, L.110, E.150, Y.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.41, A:E.150 Water bridges: A:S.41 GOL.3: 14 residues within 4Å: Chain A: L.143, F.168, P.169, A.170, V.171, S.179, L.180, S.181 Chain B: Q.165, E.166, S.167, S.181, S.182, T.183 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.181, B:S.181, B:T.183, B:T.183, A:P.169, A:S.181 GOL.4: 8 residues within 4Å: Chain B: L.42, Q.50, I.63, P.64, R.66, F.67, E.86, D.87 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.50, B:Q.50, B:Q.50, B:R.66 GOL.7: 5 residues within 4Å: Chain B: V.3, M.4, F.103, G.104, P.105 2 PLIP interactions: 2 interactions with chain B Water bridges: B:M.4, B:M.4 GOL.8: 5 residues within 4Å: Chain B: V.155, Q.160, L.186, D.190, H.194 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.160

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 3 residues within 4Å: Chain A: H.166 Chain B: N.142, N.143 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.166, H2O.1 ZN.6: 2 residues within 4Å: Chain B: D.156, H.194 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.156, B:H.194 ZN.9: 3 residues within 4Å: Chain B: R.66, E.84, E.86 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.84, B:E.86, B:E.86 ZN.10: 1 residues within 4Å: Chain C: H.10 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:H.10, H2O.1, H2O.2, H2O.3, H2O.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

2024-07-31

Peptides

Para.09 heavy chain: A
Para.09 light chain: B
Triggering receptor expressed on myeloid cells 2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

Para.09 heavy chain

Para.09 light chain

Triggering receptor expressed on myeloid cells 2

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