SMTL ID : 7t8h.1

G93A mutant of human SOD1 bound with MR6-26-2 in P21 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.63, H.71, G.72, H.80, D.83, K.136 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.4: 5 residues within 4Å: Chain A: H.46, H.48, H.63, V.118, H.120 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.46, A:H.48, A:H.63, A:H.120, H2O.3 ZN.6: 6 residues within 4Å: Chain B: H.63, H.71, G.72, 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.8: 5 residues within 4Å: Chain B: H.46, H.48, H.63, V.118, H.120 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.46, B:H.48, B:H.63, B:H.120, H2O.7

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

ACT.2: 3 residues within 4Å: Chain A: T.39, E.40, K.91 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.40, A:K.91 Hydrogen bonds: A:E.40, A:K.91

2 x Q8E: ~{N}-[(6-methoxypyridin-3-yl)methyl]-2-selanyl-benzamide(Non-covalent)

Q8E.3: 13 residues within 4Å: Chain A: T.2, L.106, S.107, G.108, C.111, I.113, G.114, I.151 Chain B: C.111, I.113, R.115, I.151 Ligands: Q8E.7 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.113, A:T.2, A:I.113, A:I.113, A:I.151, A:I.151 Hydrogen bonds: B:R.115 Water bridges: A:K.3, A:G.108 Q8E.7: 10 residues within 4Å: Chain A: R.115 Chain B: T.2, L.106, S.107, G.108, D.109, C.111, I.113, I.151 Ligands: Q8E.3 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.2, B:I.151, B:I.151 Water bridges: B:G.108 Hydrogen bonds: A:R.115

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: E.133, T.137, N.139, A.140, G.141 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.133, A:T.137, A:A.140, A:G.141 SO4.9: 5 residues within 4Å: Chain B: E.133, T.137, N.139, A.140, G.141 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.137, B:T.137, B:A.140, B:G.141 Water bridges: B:T.137, B:G.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, S. et al., Ebselen analogues delay disease onset and its course in fALS by on-target SOD-1 engagement. Sci Rep (2024)

Release Date

2023-01-25

Peptides

Superoxide dismutase [Cu-Zn]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

Superoxide dismutase [Cu-Zn]

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