SMTL ID : 6d49.1 (1 other biounit)

Cell Surface Receptor in Complex with Ligand at 1.80-A Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: P.32, Y.33, Y.34 Ligands: FVP.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.33 GOL.2: 4 residues within 4Å: Chain A: C.20, V.21, L.22, S.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.20, A:S.88 GOL.3: 3 residues within 4Å: Chain A: G.107, S.108, K.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.110 Water bridges: A:K.110, A:K.110 GOL.4: 6 residues within 4Å: Chain A: I.51, S.52, R.53, D.54, S.55, Q.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.64 Water bridges: A:D.54, A:Q.64

1 x FVP: 2-aminoethyl 5-{[(4-cyclohexyl-1H-1,2,3-triazol-1-yl)acetyl]amino}-3,5,9-trideoxy-9-[(4-hydroxy-3,5-dimethylbenzene-1-carbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->6)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside(Non-covalent)

FVP.5: 13 residues within 4Å: Chain A: D.2, N.4, F.5, I.50, S.52, F.101, R.103, K.110, Y.111, S.112, Y.113, K.114 Ligands: GOL.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.101, A:K.114, A:K.114 Hydrogen bonds: A:G.1, A:S.52, A:S.52, A:K.110, A:S.112, A:S.112, A:K.114, A:Q.117 Water bridges: A:G.48, A:I.51, A:K.110, A:K.110, A:K.114 Salt bridges: A:R.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miles, L.A. et al., Small Molecule Binding to Alzheimer Risk Factor CD33 Promotes A beta Phagocytosis. Iscience (2019)

Release Date

2019-04-17

Peptides

Myeloid cell surface antigen CD33: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myeloid cell surface antigen CD33

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