SMTL ID : 6z4l.1

A4V mutant of human SOD1 bound with 2-(pyridin-3-ylmethyl)benzoisoselenazolone derivative 9 in P21 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

Q8H.1: 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: Q8H.6 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.2, A:I.113, A:I.113, A:I.151, B:I.113 Water bridges: A:G.108, B:R.115 Hydrogen bonds: B:R.115 Q8H.6: 7 residues within 4Å: Chain A: G.108, D.109 Chain B: L.106, S.107, G.108, C.111 Ligands: Q8H.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.108

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 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: SO4.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.46, A:H.48, A:H.120 ZN.7: 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: SO4.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.46, B:H.48, B:H.120

3 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:H.46 Water bridges: A:R.143, A:R.143 Salt bridges: A:H.48, A:H.63, A:H.120, A:R.143 SO4.5: 3 residues within 4Å: Chain A: D.76, E.77, E.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.77, A:E.78 SO4.9: 8 residues within 4Å: Chain B: H.46, H.48, H.63, H.120, T.137, G.141, R.143 Ligands: ZN.8 11 PLIP interactions: 11 interactions with chain B Water bridges: B:T.137, B:T.137, B:G.141, B:R.143, 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]

Related Entries With Identical Sequence