SMTL ID : 8e0p.4 (3 other biounits)

Crystal structure of mouse APCDD1 in fusion with engineered MBP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

monomer

Ligands

1 x BGC- GLC: alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-GLC.1: 15 residues within 4Å: Chain A: N.15, D.17, K.18, W.65, A.66, D.68, R.69, E.114, E.156, P.157, Y.158, F.159, W.233, M.333, W.343 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.15, A:D.17, A:K.18, A:E.114, A:E.114, A:E.114, A:W.65, A:R.69, A:R.69, A:Y.158 Salt bridges: A:K.18

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

NAG.2: 3 residues within 4Å: Chain A: Y.425, N.427, T.429 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.429 Hydrogen bonds: A:T.429 NAG.3: 1 residues within 4Å: Chain A: N.495 No protein-ligand interaction detected (PLIP) NAG.4: 5 residues within 4Å: Chain A: H.643, N.645, N.646, T.648, R.673 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.645, A:N.646

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: W.649, Y.653, F.691, E.748, E.750, F.752, R.769 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.750, A:E.750, A:R.769

1 x DMX: 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE(Non-covalent)

DMX.6: 6 residues within 4Å: Chain A: P.94, F.95, V.262, A.327, Q.328, I.332 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.94, A:P.94, A:F.95 pi-Cation interactions: A:F.95

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

CL.7: 6 residues within 4Å: Chain A: R.630, R.638, F.640, Y.653, N.766, Q.787 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsieh, F.L. et al., Structure of WNT inhibitor adenomatosis polyposis coli down-regulated 1 (APCDD1), a cell-surface lipid-binding protein. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-05-03

Peptides

Maltodextrin-binding protein, Protein APCDD1 complex: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Maltodextrin-binding protein, Protein APCDD1 complex

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