SMTL ID : 3umi.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

ACT.1: 3 residues within 4Å: Chain A: E.69, E.72 Ligands: CD.7 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: H.89, H.139, H.143 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.89, A:H.139, A:H.143, H2O.4

8 x CD: CADMIUM ION(Non-covalent)

CD.3: 4 residues within 4Å: Chain A: E.94, N.98, D.136, H.165 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.94, A:D.136, A:H.165, H2O.2 CD.4: 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.2 CD.5: 1 residues within 4Å: Chain A: H.146 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.146 CD.6: 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.7: 3 residues within 4Å: Chain A: E.69, E.72 Ligands: ACT.1 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.1 CD.8: 2 residues within 4Å: Chain A: Q.191, D.195 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.195, A:D.195 CD.9: 1 residues within 4Å: Chain A: H.66 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.66 CD.10: 2 residues within 4Å: Chain A: E.28, E.31 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.28, A:E.31

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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