SMTL ID : 5in2.1

Crystal structure of extra cellular Cu/Zn Superoxide Dismutase from Onchocerca volvulus at 1.5 Angstrom; Insight into novel binding site and new inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: R.9, G.10, G.13, V.14, S.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.10, A:G.13 Water bridges: A:V.14 GOL.8: 5 residues within 4Å: Chain B: R.9, G.10, G.13, V.14, S.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.10, B:G.13 Water bridges: B:V.14

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.63, H.71, H.80, D.83 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.9: 4 residues within 4Å: Chain B: H.63, H.71, H.80, D.83 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.3: 6 residues within 4Å: Chain A: H.46, H.48, H.63, V.118, H.120 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.46, A:H.48, A:H.120 CU.10: 6 residues within 4Å: Chain B: H.46, H.48, H.63, V.118, H.120 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.46, B:H.48, B:H.120

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

SO4.4: 8 residues within 4Å: Chain A: H.46, H.48, D.62, H.63, H.120, T.140, R.146 Ligands: CU.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.140 Water bridges: A:T.140, A:G.144, A:R.146, A:R.146 Salt bridges: A:H.46, A:H.48, A:H.63, A:H.120, A:R.146 SO4.11: 8 residues within 4Å: Chain B: H.46, H.48, D.62, H.63, H.120, T.140, R.146 Ligands: CU.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.140 Water bridges: B:D.62, B:T.140, B:G.144, B:R.146 Salt bridges: B:H.46, B:H.48, B:H.63, B:H.120, B:R.146

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

CL.5: 4 residues within 4Å: Chain A: G.23, S.24, S.27, I.28 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: G.23, S.24, S.27, I.28 Ligand excluded by PLIP

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 8 residues within 4Å: Chain A: P.40, G.41, L.42, V.88, A.89, G.90, A.91, T.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.42, A:T.123 PGE.13: 8 residues within 4Å: Chain B: P.40, G.41, L.42, V.88, A.89, G.90, A.91, T.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.42, B:T.123

2 x AZI: AZIDE ION(Non-covalent)

AZI.7: 4 residues within 4Å: Chain A: P.74, G.85, N.86, L.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.86, A:N.86 Water bridges: A:N.86 AZI.14: 4 residues within 4Å: Chain B: P.74, G.85, N.86, L.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.86, B:N.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moustafa, A. et al., Crystal structure of extracellular Cu/Zn Superoxide Dismutase from Onchocerca volvulus at 1.5 Angstrom; Insight into novel binding site and new inhibitors. To Be Published

Release Date

2017-03-29

Peptides

Extracellular superoxide dismutase [Cu-Zn]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Extracellular superoxide dismutase [Cu-Zn]