SMTL ID : 6z4j.1

A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 5 in P21 space group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.63, H.71, H.80, D.83 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.63, A:H.71, A:H.80, A:D.83, A:D.83 ZN.3: 5 residues within 4Å: Chain A: H.46, H.48, H.63, H.120 Ligands: CL.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.46, A:H.48, A:H.120 ZN.5: 5 residues within 4Å: Chain B: H.63, H.71, H.80, D.83, K.136 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.63, B:H.71, B:H.80, B:D.83, B:D.83 ZN.7: 5 residues within 4Å: Chain B: H.46, H.48, H.63, H.120 Ligands: CL.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.46, B:H.48, B:H.120, H2O.5

2 x Q7W: ~{N}-[(3-chlorophenyl)methyl]-2-selanyl-benzamide(Non-covalent)

Q7W.2: 9 residues within 4Å: Chain A: T.2, L.106, S.107, C.111, I.113, I.151 Chain B: I.113, R.115 Ligands: Q7W.6 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.113, A:I.151, B:I.113 pi-Cation interactions: B:R.115 Q7W.6: 9 residues within 4Å: Chain A: R.115 Chain B: T.2, L.106, S.107, G.108, C.111, I.113, I.151 Ligands: Q7W.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B pi-Cation interactions: A:R.115 Hydrophobic interactions: B:I.151

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

CL.4: 5 residues within 4Å: Chain A: H.48, H.63, H.120, R.143 Ligands: ZN.3 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: H.48, H.63, H.120, R.143 Ligands: ZN.7 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amporndanai, K. et al., Novel Selenium-based compounds with therapeutic potential for SOD1-linked amyotrophic lateral sclerosis. Ebiomedicine (2020)

Release Date

2020-09-16

Peptides

Superoxide dismutase [Cu-Zn]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Superoxide dismutase [Cu-Zn]

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