SMTL ID : 5yto.1 (4 other biounits)

Crystal Structure of human Superoxide Dismutase I (hSOD1) in complex with a napthalene-catechol linked compound.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.90, H.98, H.107, D.110, K.163 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.90, A:H.98, A:H.107, A:D.110 ZN.3: 5 residues within 4Å: Chain B: H.90, H.98, H.107, D.110, K.163 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.90, B:H.98, B:H.107, B:D.110, B:D.110

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: H.75, H.90, H.147, T.164, G.168, R.170 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.90, A:R.170 Water bridges: A:K.163, A:K.163, A:T.164, A:T.164, A:R.170 GOL.4: 6 residues within 4Å: Chain B: H.75, H.90, H.147, T.164, G.168, R.170 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.90, B:R.170 Water bridges: B:T.164, B:R.170, B:R.170

1 x 946: 4-[(1~{R})-2-(naphthalen-2-ylmethylamino)-1-oxidanyl-ethyl]benzene-1,2-diol(Non-covalent)

946.5: 7 residues within 4Å: Chain B: E.48, Q.49, K.50, P.55, K.57, W.59, E.127 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:K.57, B:W.59 Hydrogen bonds: B:E.48, B:K.50, B:P.55, B:P.55, B:E.127 Water bridges: B:E.51 pi-Stacking: B:W.59, B:W.59, B:W.59

1 x PS5: PENTASULFIDE-SULFUR(Non-covalent)

PS5.6: 6 residues within 4Å: Chain A: C.138, I.140, I.178 Chain B: L.133, C.138, I.140 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manjula, R. et al., Assessment of ligand binding at a site relevant to SOD1 oxidation and aggregation. FEBS Lett. (2018)

Release Date

2018-11-21

Peptides

Superoxide dismutase [Cu-Zn]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Superoxide dismutase [Cu-Zn]

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