SMTL ID : 5o3y.1

SOD1 bound to Ebsulfur

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 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: SO4.4 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.6: 5 residues within 4Å: Chain B: H.46, H.48, H.63, H.120 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.46, B:H.48, B:H.120

2 x 9JK: ~{N}-phenyl-2-sulfanyl-benzamide(Non-covalent)

9JK.2: 7 residues within 4Å: Chain A: L.106, S.107, G.108, C.111, I.113 Chain B: I.151 Ligands: 9JK.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.113, B:I.151 Hydrogen bonds: A:G.108 9JK.7: 9 residues within 4Å: Chain A: I.113, I.151 Chain B: L.106, S.107, G.108, D.109, C.111, I.113 Ligands: 9JK.2 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:D.109, B:I.113, A:I.113, A:I.151 Hydrogen bonds: B:G.108

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

SO4.4: 7 residues within 4Å: Chain A: H.46, H.48, H.63, H.120, T.137, R.143 Ligands: ZN.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.137 Water bridges: A:H.63 Salt bridges: A:H.46, A:H.48, A:H.63, A:H.120, A:R.143 SO4.8: 7 residues within 4Å: Chain B: H.46, H.48, H.63, H.120, T.137, R.143 Ligands: ZN.6 8 PLIP interactions: 8 interactions with chain B Water bridges: B:H.63, B:T.137, B:G.141, B:R.143 Salt bridges: B:H.48, B:H.63, B:H.120, B:R.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Capper, M.J. et al., The cysteine-reactive small molecule ebselen facilitates effective SOD1 maturation. Nat Commun (2018)

Release Date

2018-06-13

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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