SMTL ID : 6spj.2 (2 other biounits)

A4V MUTANT OF HUMAN SOD1 WITH EBSELEN DERIVATIVE 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 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: CL.13 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.2 ZN.14: 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.16: 5 residues within 4Å: Chain B: H.46, H.48, H.63, H.120 Ligands: GOL.20 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

2 x LR2: ~{N}-pyridin-2-yl-2-selanyl-benzamide(Non-covalent)

LR2.2: 7 residues within 4Å: Chain A: L.106, S.107, G.108, C.111, I.113 Chain B: I.151 Ligands: LR2.15 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.151 Hydrogen bonds: A:G.108, A:G.108 LR2.15: 6 residues within 4Å: Chain B: L.106, S.107, G.108, C.111, I.113 Ligands: LR2.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.108

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

SO4.4: 2 residues within 4Å: Chain A: L.67, R.69 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.69 SO4.5: 1 residues within 4Å: Chain A: K.75 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.75 SO4.6: 2 residues within 4Å: Chain A: D.90, K.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.91 Water bridges: A:D.90 SO4.7: 2 residues within 4Å: Chain A: N.19, W.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.32 Water bridges: A:W.32 SO4.17: 4 residues within 4Å: Chain B: G.41, L.42, A.123 Ligands: SO4.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.42, B:L.42 SO4.18: 3 residues within 4Å: Chain B: K.122, A.123 Ligands: SO4.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.123 SO4.19: 3 residues within 4Å: Chain B: E.40, D.90, K.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.91

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: D.76, E.77, E.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.77, A:E.78 Water bridges: A:D.76, A:D.76 GOL.20: 7 residues within 4Å: Chain B: H.48, P.62, H.63, H.120, T.137, R.143 Ligands: ZN.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.63, B:T.137, B:R.143, B:R.143

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.9: 6 residues within 4Å: Chain A: K.122, E.133, T.137, N.139, A.140, G.141 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.133, A:N.139, A:A.140, A:G.141 Salt bridges: A:E.133 DMS.10: 3 residues within 4Å: Chain A: T.58, S.142, R.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.143 Water bridges: A:T.58 DMS.11: 4 residues within 4Å: Chain A: Q.15, G.16, I.17, K.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.15 DMS.12: 3 residues within 4Å: Chain A: G.41, L.42, A.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.42

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 5 residues within 4Å: Chain A: H.48, H.120, T.137, R.143 Ligands: ZN.3 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: G.147, V.148 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chantadul, V. et al., Ebselen as template for stabilization of A4V mutant dimer for motor neuron disease therapy. Commun Biol (2020)

Release Date

2020-03-18

Peptides

Superoxide dismutase [Cu-Zn]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Superoxide dismutase [Cu-Zn]

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