SMTL ID : 7t8g.1

G93A mutant of human SOD1 bound with MR6-8-2 in P21 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.63, H.71, 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.3: 5 residues within 4Å: Chain A: H.46, H.48, H.63, H.120 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.46, A:H.48, A:H.120 ZN.7: 4 residues within 4Å: Chain B: H.63, H.71, H.80, D.83 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, H.120 Ligands: SO4.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.46, B:H.48, B:H.120

2 x Q8H: ~{N}-(pyridin-3-ylmethyl)-2-selanyl-benzamide(Non-covalent)

Q8H.2: 10 residues within 4Å: Chain A: T.2, L.106, S.107, C.111, I.113, I.151 Chain B: I.113, R.115 Ligands: Q8H.6, SE.9 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.113, A:I.151, B:I.113 Water bridges: B:R.115 Q8H.6: 7 residues within 4Å: Chain A: G.108, D.109 Chain B: S.107, G.108, C.111 Ligands: Q8H.2, SE.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.108

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

ACT.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

SO4.5: 7 residues within 4Å: Chain A: H.46, H.48, H.63, H.120, T.137, R.143 Ligands: ZN.3 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.143, A:R.143, A:R.143 Salt bridges: A:H.46, A:H.48, A:H.63, A:H.120, A:R.143 SO4.10: 8 residues within 4Å: Chain B: H.46, H.48, H.63, H.120, T.137, G.141, R.143 Ligands: ZN.8 10 PLIP interactions: 10 interactions with chain B Water bridges: B:H.63, B:T.137, B:R.143, B:R.143, B:R.143 Salt bridges: B:H.46, B:H.48, B:H.63, B:H.120, B:R.143

1 x SE: SELENIUM ATOM(Non-covalent)

SE.9: 5 residues within 4Å: Chain B: L.106, C.111, I.113 Ligands: Q8H.2, Q8H.6 No protein-ligand interaction detected (PLIP)

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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