SMTL ID : 5ud7.1

Crystal Structure of Wild-Type Ig-like Domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 7 residues within 4Å: Chain A: R.44, V.45, V.46, S.47, R.59, N.61 Chain D: P.19 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Water bridges: D:G.72 Hydrogen bonds: A:S.47, A:N.61 NAG.3: 7 residues within 4Å: Chain B: V.45, V.46, S.47, R.59, N.61 Chain E: P.19, G.72 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain B Water bridges: E:Y.20, E:Y.20 Hydrogen bonds: B:S.47, B:N.61 NAG.5: 5 residues within 4Å: Chain C: R.44, V.45, N.61 Chain F: P.19, G.73 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.43, C:N.61 Hydrophobic interactions: F:P.19 NAG.7: 3 residues within 4Å: Chain D: Q.43, V.45, N.61 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.43 NAG.11: 2 residues within 4Å: Chain E: V.45, N.61 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain F: Q.43, R.44, V.45, N.61 No protein-ligand interaction detected (PLIP)

5 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 3 residues within 4Å: Chain B: L.51, W.52, L.53 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain C: L.51, W.52, L.53 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain E: L.51, W.52, L.53 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain E: R.28 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain E: R.44, S.47 Ligand excluded by PLIP

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

SO4.6: 9 residues within 4Å: Chain B: G.11, Q.12, S.13, R.80, N.81 Chain C: S.17, C.18, P.19, T.74 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.17, C:T.74, B:N.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sudom, A. et al., Molecular basis for the loss-of-function effects of the Alzheimer's disease-associated R47H variant of the immune receptor TREM2. J. Biol. Chem. (2018)

Release Date

2018-04-04

Peptides

Triggering receptor expressed on myeloid cells 2: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Triggering receptor expressed on myeloid cells 2

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