SMTL ID : 4rda.1

X-RAY STRUCTURE OF THE AMYLOID PRECURSOR PROTEIN-LIKE PROTEIN 1 (APLP1) E2 DOMAIN IN COMPLEX WITH A HEPARIN DODECASACCHARIDE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

1 x IDS- SGN- IDS- SGN- UAP: 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid(Non-covalent)

IDS-SGN-IDS-SGN-UAP.1: 15 residues within 4Å: Chain A: H.22, F.25, K.29, R.84, V.88, H.91, V.95, H.141, R.144, H.145, H.148 Chain B: K.29, R.84, H.148 Ligands: IDS-SGN-IDS-SGN-IDS-SGN.2 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.91 Water bridges: A:R.144, A:R.144, A:R.144, B:R.84, B:R.84, B:R.84, A:R.84 Salt bridges: A:H.141, A:H.141, A:H.145, A:H.148, A:H.148, B:K.29, B:R.84, A:K.29, A:R.84, A:H.148, B:H.148 Hydrophobic interactions: A:V.88

1 x IDS- SGN- IDS- SGN- IDS- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid

IDS-SGN-IDS-SGN-IDS-SGN.2: 13 residues within 4Å: Chain A: L.26, K.29 Chain B: H.22, H.91, V.95, R.130, R.133, H.141, R.144, H.145, H.148 Ligands: IDS-SGN-IDS-SGN-UAP.1, IDS-SGN-IDS-SGN-UAP.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:R.144, B:H.148 Salt bridges: B:H.22, B:H.141, A:K.29

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 1 residues within 4Å: Chain A: H.201 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.201, H2O.1, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dahms, S.O. et al., Interaction of the amyloid precursor protein-like protein 1 (APLP1) E2 domain with heparan sulfate involves two distinct binding modes. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-03-11

Peptides

Amyloid-like protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Amyloid-like protein 1