SMTL ID : 8ccx.1

Human SOD1 in complex with S-XL6 cross-linker

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

2 x CU: COPPER (II) ION(Non-covalent)

CU.1: 7 residues within 4Å: Chain A: H.47, H.49, H.64, V.119, H.121 Ligands: ZN.2, SO4.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.47, A:H.49, A:H.121 CU.6: 6 residues within 4Å: Chain B: H.47, H.49, H.64, V.119, H.121 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.47, B:H.49, B:H.64, B:H.121

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: H.47, H.49, H.64, V.119, H.121 Ligands: CU.1, SO4.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.47, A:H.49, A:H.121 ZN.3: 4 residues within 4Å: Chain A: H.64, H.72, H.81, D.84 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.64, A:H.72, A:H.81, A:D.84, A:D.84 ZN.7: 6 residues within 4Å: Chain B: H.47, H.49, H.64, V.119, H.121 Ligands: CU.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.47, B:H.49, B:H.121, H2O.8 ZN.8: 5 residues within 4Å: Chain B: H.64, H.72, H.81, D.84, K.137 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.64, B:H.72, B:H.81, B:D.84, B:D.84

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

SO4.4: 9 residues within 4Å: Chain A: H.47, H.49, H.64, H.121, T.138, G.142, R.144 Ligands: CU.1, ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.138 Water bridges: A:G.142, A:R.144, A:R.144, A:R.144 Salt bridges: A:H.49, A:H.64, A:H.121, A:R.144 SO4.9: 6 residues within 4Å: Chain B: K.123, E.134, T.138, N.140, A.141, G.142 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.138, B:T.138, B:N.140, B:A.141, B:G.142, B:G.142 Water bridges: B:K.123, B:N.140 Salt bridges: B:K.123

1 x UDI: butane-1,4-dithiol(Non-covalent)

UDI.5: 10 residues within 4Å: Chain A: L.107, S.108, C.112, I.114, I.152 Chain B: L.107, S.108, G.109, C.112, I.114 No protein-ligand interaction detected (PLIP)

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

DMS.10: 6 residues within 4Å: Chain B: A.56, G.57, C.58, T.59, S.60, R.144 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.58, B:T.59 Water bridges: B:R.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hossain, M.A. et al., Evaluating protein cross-linking as a therapeutic strategy to stabilize SOD1 variants in a mouse model of familial ALS. Plos Biol. (2024)

Release Date

2023-12-13

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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