SMTL ID : 5oc0.1

Structure of E. coli superoxide oxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 19 residues within 4Å: Chain A: Y.5, H.13, W.14, F.17, V.20, R.59, R.63, H.87, I.90, Y.91, F.94, I.148, H.151, A.155, T.166, L.167, R.169, M.170 Ligands: GOL.4 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Y.5, A:W.14, A:W.14, A:F.17, A:F.17, A:V.20, A:Y.91, A:F.94, A:I.148, A:T.166 Water bridges: A:H.13, A:R.59, A:R.169 Salt bridges: A:R.59, A:H.87, A:R.169 Metal complexes: A:H.13, A:H.151 HEM.2: 20 residues within 4Å: Chain A: Y.24, M.27, R.30, H.45, V.46, G.49, I.50, I.52, F.94, L.97, P.98, G.101, L.102, M.105, R.108, W.112, K.134, H.137, E.138, A.141 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:Y.24, A:Y.24, A:V.46, A:V.46, A:I.52, A:F.94, A:L.97, A:L.97, A:P.98, A:L.102, A:W.112, A:A.141 Hydrogen bonds: A:E.138 Water bridges: A:R.108 Salt bridges: A:R.30, A:R.108, A:K.134 pi-Stacking: A:H.45 Metal complexes: A:H.45, A:H.137

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: R.63, L.64, Y.66 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:R.63, A:L.64, A:Y.66

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: H.87, I.90, H.151 Ligands: HEM.1 No protein-ligand interaction detected (PLIP)

1 x 37X: Octyl Glucose Neopentyl Glycol(Non-covalent)

37X.5: 5 residues within 4Å: Chain A: F.29, F.32, F.33, P.34, D.37 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.29, A:F.33 Hydrogen bonds: A:D.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lundgren, C.A.K. et al., Scavenging of superoxide by a membrane-bound superoxide oxidase. Nat. Chem. Biol. (2018)

Release Date

2018-06-20

Peptides

Cytochrome b561: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b561