SMTL ID : 6b8o.1

WT Ig-like V Domain with Phosphatidylserine

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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.47 NAG.12: 9 residues within 4Å: Chain B: R.44, V.45, V.46, S.47, R.59, N.61 Chain E: P.19, G.72 Ligands: SO4.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.47, B:N.61 NAG.20: 7 residues within 4Å: Chain C: R.44, V.45, N.61 Chain F: P.19, G.72, G.73 Ligands: SO4.35 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Water bridges: C:Q.43 Hydrophobic interactions: F:P.19 NAG.23: 3 residues within 4Å: Chain D: Q.43, V.45, N.61 No protein-ligand interaction detected (PLIP) NAG.28: 3 residues within 4Å: Chain E: Q.43, V.45, N.61 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.43, E:N.61 NAG.33: 4 residues within 4Å: Chain F: R.44, V.45, N.61 Ligands: SO4.34 No protein-ligand interaction detected (PLIP)

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

IOD.2: 3 residues within 4Å: Chain A: L.51, W.52, L.53 Ligand excluded by PLIP IOD.3: 4 residues within 4Å: Chain A: S.17, P.19 Chain C: S.13, N.81 Ligand excluded by PLIP IOD.4: 5 residues within 4Å: Chain A: S.13, R.80, N.81 Chain B: S.17, P.19 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain B: L.51, W.52, L.53 Ligand excluded by PLIP IOD.14: 4 residues within 4Å: Chain B: S.13, N.81 Chain C: S.17, P.19 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain C: L.51, W.52, L.53 Ligand excluded by PLIP IOD.29: 5 residues within 4Å: Chain C: K.24 Chain E: S.13, Q.15, R.58, R.80 Ligand excluded by PLIP

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

SO4.5: 3 residues within 4Å: Chain A: Q.83, P.84, H.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.85 Salt bridges: A:H.85 SO4.6: 5 residues within 4Å: Chain A: M.23, K.24 Chain F: S.13, T.78, R.80 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.13 Water bridges: F:R.80 Salt bridges: F:R.80 SO4.24: 4 residues within 4Å: Chain D: Y.20, D.21, K.24, H.25 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.21 Salt bridges: D:K.24, D:H.25 SO4.25: 3 residues within 4Å: Chain D: W.26, R.28, H.96 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.28 SO4.26: 3 residues within 4Å: Chain D: D.21, M.23, K.24 No protein-ligand interaction detected (PLIP) SO4.30: 4 residues within 4Å: Chain E: R.29, R.44, S.47, L.95 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.47 Salt bridges: E:R.29, E:R.44 SO4.31: 4 residues within 4Å: Chain E: Y.20, D.21, K.24, H.25 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.21 Salt bridges: E:K.24, E:H.25 SO4.32: 8 residues within 4Å: Chain B: R.29, S.47, N.50, R.59 Chain E: Y.20, D.21, S.22 Ligands: NAG.12 7 PLIP interactions: 2 interactions with chain E, 5 interactions with chain B Hydrogen bonds: E:Y.20, E:S.22, B:R.29, B:S.47, B:S.47, B:N.50 Salt bridges: B:R.59 SO4.34: 4 residues within 4Å: Chain F: R.34, L.36, Q.43 Ligands: NAG.33 No protein-ligand interaction detected (PLIP) SO4.35: 9 residues within 4Å: Chain C: R.29, S.47, N.50, R.59 Chain F: Y.20, D.21, S.22, G.72 Ligands: NAG.20 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:R.29, C:R.29, C:S.47, C:N.50, F:S.22, F:G.72 Salt bridges: C:R.59 SO4.36: 5 residues within 4Å: Chain F: Y.20, D.21, K.24, H.25, L.103 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.21 Water bridges: F:K.24 Salt bridges: F:K.24, F:H.25

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

EDO.7: 6 residues within 4Å: Chain A: R.58, A.65, I.66, T.67, T.76, T.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.65, A:T.67, A:T.78 EDO.8: 4 residues within 4Å: Chain A: R.80 Chain B: P.19, Y.20, D.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.80, A:R.80 EDO.9: 3 residues within 4Å: Chain A: R.29, R.44, L.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.29, A:R.44, A:R.44 EDO.10: 3 residues within 4Å: Chain A: W.26, W.52, T.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.70, A:T.70 EDO.11: 3 residues within 4Å: Chain A: L.57, R.58 Chain D: L.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.58 Water bridges: A:R.58 EDO.16: 5 residues within 4Å: Chain B: W.52, L.53, T.70, L.71 Chain D: F.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.70, B:T.70 EDO.17: 4 residues within 4Å: Chain B: F.56, L.57, R.58 Chain E: L.71 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.58 EDO.18: 4 residues within 4Å: Chain B: V.45, N.61, S.63, T.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.63, B:T.64, B:T.64 EDO.19: 2 residues within 4Å: Chain B: R.80 Chain C: Y.20 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:S.22 Hydrogen bonds: B:R.80 EDO.37: 4 residues within 4Å: Chain F: T.3, L.103, R.104, K.105 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.3, F:K.105, F:K.105

3 x PSF: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE(Non-covalent)

PSF.15: 12 residues within 4Å: Chain B: H.49, N.50, L.51, L.54, F.56, L.57, R.59 Chain E: S.22, M.23, W.26, T.70, L.71 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain E Hydrophobic interactions: B:L.54, B:F.56, B:L.57 Hydrogen bonds: B:N.50, B:N.50, E:S.22, E:T.70, E:L.71 Salt bridges: B:H.49, B:H.49, B:H.49, B:R.59 Water bridges: E:T.70 PSF.22: 12 residues within 4Å: Chain C: H.49, N.50, L.51, L.54, F.56, L.57, R.59 Chain F: S.22, M.23, W.26, T.70, L.71 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain F Hydrophobic interactions: C:F.56, C:F.56, C:L.57 Hydrogen bonds: C:N.50, C:N.50, F:S.22, F:T.70, F:T.70 Salt bridges: C:H.49, C:H.49, C:H.49, C:R.59 PSF.27: 11 residues within 4Å: Chain A: H.49, N.50, L.51, L.54, F.56 Chain D: S.22, M.23, W.26, W.52, T.70, L.71 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.51, A:L.54, A:L.54, A:F.56 Hydrogen bonds: A:N.50, D:S.22, D:T.70 Salt bridges: A:H.49, A:H.49

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

2018-06-27

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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