SMTL ID : 3umh.1

X-ray structure of the E2 domain of the human amyloid precursor protein (APP) in complex with cadmium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: R.82, V.86, H.146 Ligands: CD.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.86 Salt bridges: A:H.146 ACT.2: 3 residues within 4Å: Chain A: E.69, E.72 Ligands: CD.8 No protein-ligand interaction detected (PLIP)

9 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.3: 4 residues within 4Å: Chain A: H.20, H.89, H.139, H.143 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.89, A:H.139, A:H.143 CD.4: 4 residues within 4Å: Chain A: E.94, N.98, D.136, H.165 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.94, A:D.136, A:D.136, A:H.165, H2O.3 CD.5: 1 residues within 4Å: Chain A: D.151 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.151, A:D.151, H2O.4 CD.6: 2 residues within 4Å: Chain A: H.146 Ligands: ACT.1 3 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.146, ACT.1, H2O.3 CD.7: 2 residues within 4Å: Chain A: H.34, E.75 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.34, A:E.75, A:E.75, H2O.1 CD.8: 3 residues within 4Å: Chain A: E.69, E.72 Ligands: ACT.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.69, A:E.69, A:E.72, A:E.72, ACT.2 CD.9: 1 residues within 4Å: Chain A: H.66 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.66, H2O.3, H2O.4 CD.10: 1 residues within 4Å: Chain A: D.195 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.195, A:D.195, H2O.3 CD.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dahms, S.O. et al., Metal Binding Dictates Conformation and Function of the Amyloid Precursor Protein (APP) E2 Domain. J.Mol.Biol. (2012)

Release Date

2012-01-25

Peptides

Amyloid beta A4 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Amyloid beta A4 protein

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