SMTL ID : 2wyz.1

L38V SOD1 mutant complexed with UMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.46, H.48, H.63, H.120 Ligands: CU.2, SO4.4 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.7 ZN.3: 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.7: 6 residues within 4Å: Chain B: H.46, H.48, H.63, H.120 Ligands: CU.6, SO4.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.46, B:H.48, B:H.120 ZN.8: 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

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

CU.2: 6 residues within 4Å: Chain A: H.46, H.48, H.63, H.120 Ligands: ZN.1, SO4.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.46, A:H.48, A:H.120 CU.6: 6 residues within 4Å: Chain B: H.46, H.48, H.63, H.120 Ligands: ZN.7, SO4.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.46, B:H.48, B:H.120

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

SO4.4: 9 residues within 4Å: Chain A: H.46, H.48, H.63, H.120, T.137, R.143 Ligands: ZN.1, CU.2, SO4.11 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.137 Water bridges: A:H.63, A:R.143, A:R.143, A:R.143 Salt bridges: A:H.48, A:H.63, A:H.120, A:R.143 SO4.9: 10 residues within 4Å: Chain B: H.46, H.48, H.63, H.120, T.137, G.141, R.143 Ligands: CU.6, ZN.7, SO4.10 9 PLIP interactions: 9 interactions with chain B Water bridges: B:A.140, 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 SO4.10: 6 residues within 4Å: Chain B: E.133, T.137, N.139, A.140, G.141 Ligands: SO4.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.139, B:A.140, B:G.141 Water bridges: B:G.141 SO4.11: 5 residues within 4Å: Chain A: T.137, N.139, A.140, G.141 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.137, A:A.140, A:G.141 Water bridges: A:N.139

1 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.5: 6 residues within 4Å: Chain A: G.73, P.74, K.75, D.76, L.126, K.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.75, A:D.76, A:D.76, A:K.128 Water bridges: A:N.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antonyuk, S.V. et al., Structural Discovery of Small Molecule Binding Sites in Cu-Zn Human Superoxide Dismutase Familial Amyotrophic Lateral Sclerosis Mutants Provides Insights for Lead Optimization. J.Med.Chem. (2010)

Release Date

2010-10-27

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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