SMTL ID : 6z3v.1

A4V mutant of human SOD1 bound with N-aryl benzoisoselenazolone derivative 13 in P21 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 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.6: 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.8: 5 residues within 4Å: Chain B: H.46, H.48, H.63, H.120 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.46, B:H.48, B:H.120

2 x Q6H: 5-fluoranyl-~{N}-(3-morpholin-4-ylcarbonylphenyl)-2-selanyl-benzamide(Non-covalent)

Q6H.2: 7 residues within 4Å: Chain A: L.106, S.107, G.108, C.111, I.113 Chain B: I.113 Ligands: Q6H.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.108 Q6H.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: Q6H.2 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:G.108

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

SO4.4: 6 residues within 4Å: Chain A: E.133, T.137, N.139, A.140, G.141 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.139, A:G.141 Water bridges: A:K.122 SO4.5: 8 residues within 4Å: Chain A: H.48, H.63, H.120, T.137, G.141, R.143 Ligands: ZN.3, SO4.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.46 Water bridges: A:R.143, A:R.143 Salt bridges: A:H.48, A:H.63, A:H.120, A:R.143 SO4.9: 6 residues within 4Å: Chain B: E.133, T.137, N.139, A.140, G.141 Ligands: SO4.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.133, B:T.137, B:A.140, B:G.141 SO4.10: 1 residues within 4Å: Chain B: K.70 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.70 SO4.11: 9 residues within 4Å: Chain B: H.46, H.48, H.63, H.120, T.137, G.141, R.143 Ligands: ZN.8, SO4.9 8 PLIP interactions: 8 interactions with chain B Water bridges: B:G.141, B:R.143, B:R.143, 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

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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