SMTL ID : 6bcs.1

LilrB2 D1D2 domains complexed with benzamidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

4 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.1: 6 residues within 4Å: Chain A: Y.99, P.100, V.126, A.127, F.128, D.178 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.100, A:V.126, A:F.128 Hydrogen bonds: A:D.178 BEN.2: 6 residues within 4Å: Chain A: Y.39, E.41, R.73, Y.74, G.75 Ligands: DMS.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.41 BEN.3: 6 residues within 4Å: Chain A: I.132, C.144, N.146, Y.177, P.182, W.185 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.132, A:P.182, A:W.185 Hydrogen bonds: A:N.146 Water bridges: A:N.146, A:N.146 pi-Stacking: A:Y.177 BEN.4: 6 residues within 4Å: Chain A: D.14, S.15, V.16, C.134, P.142, C.144 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.16, A:P.142, A:P.142 Hydrogen bonds: A:D.14, A:S.15

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: Q.19, T.67, W.68, M.95 Ligands: DMS.7 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: A.157, I.158 Ligand excluded by PLIP

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 4 residues within 4Å: Chain A: W.68, Y.99, V.184 Ligands: CL.5 No protein-ligand interaction detected (PLIP) DMS.8: 2 residues within 4Å: Chain A: R.73 Ligands: BEN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.73, A:R.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, Q. et al., Inhibiting amyloid-beta cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design. Nat Chem (2018)

Release Date

2018-09-05

Peptides

Leukocyte immunoglobulin-like receptor subfamily B member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Leukocyte immunoglobulin-like receptor subfamily B member 2