SMTL ID : 6n9h.1

De novo designed homo-trimeric amantadine-binding protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.04 Å

Oligo State

homo-trimer

Ligands

3 x 308: (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine(Non-covalent)

308.1: 14 residues within 4Å: Chain A: I.69, L.72, A.73, S.76 Chain B: I.69, L.72, A.73, S.76 Chain C: I.69, L.72, A.73, S.76 Ligands: 308.3, 308.5 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:L.72, A:L.72, B:L.72 Hydrogen bonds: C:S.76 308.3: 14 residues within 4Å: Chain A: I.69, L.72, A.73, S.76 Chain B: I.69, L.72, A.73, S.76 Chain C: I.69, L.72, A.73, S.76 Ligands: 308.1, 308.5 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:L.72, A:L.72, B:L.72 Hydrogen bonds: A:S.76 308.5: 14 residues within 4Å: Chain A: I.69, L.72, A.73, S.76 Chain B: I.69, L.72, A.73, S.76 Chain C: I.69, L.72, A.73, S.76 Ligands: 308.1, 308.3 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:L.72, B:L.72, A:L.72 Hydrogen bonds: B:S.76

3 x NA: SODIUM ION(Non-functional Binders)

NA.2: 8 residues within 4Å: Chain A: N.52, N.55 Chain B: N.52, N.55 Chain C: N.52, N.55 Ligands: NA.4, NA.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.52 NA.4: 8 residues within 4Å: Chain A: N.52, N.55 Chain B: N.52, N.55 Chain C: N.52, N.55 Ligands: NA.2, NA.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.52 NA.6: 8 residues within 4Å: Chain A: N.52, N.55 Chain B: N.52, N.55 Chain C: N.52, N.55 Ligands: NA.2, NA.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., De novo design of a homo-trimeric amantadine-binding protein. Elife (2019)

Release Date

2019-12-18

Peptides

amantadine-binding protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

amantadine-binding protein

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