SMTL ID : 6xoj.1

ScoE with the CABA substrate bound and alpha-ketoglutarate in an off-site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x 7UC: (3~{R})-3-(2-hydroxy-2-oxoethylamino)butanoic acid(Non-covalent)

7UC.1: 12 residues within 4Å: Chain A: Y.96, Y.101, T.127, G.128, F.130, D.134, Y.135, F.137, K.193, F.239, R.310 Ligands: AKG.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.101, A:F.130, A:F.239 Hydrogen bonds: A:Y.101, A:G.128, A:Y.135 Water bridges: A:K.193, A:R.310 Salt bridges: A:K.193, A:R.310

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 11 residues within 4Å: Chain A: F.110, T.127, G.128, F.130, H.132, D.134, F.239, H.295, R.310 Ligands: 7UC.1, FE.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.110 Hydrogen bonds: A:T.127, A:G.128, A:R.310 Water bridges: A:R.310 Salt bridges: A:H.132, A:H.132, A:H.295

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: E.35, S.63, T.64, T.67 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.64, A:T.64 ACT.4: 3 residues within 4Å: Chain A: M.31, Q.32, I.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.33

1 x FE: FE (III) ION(Non-covalent)

FE.5: 5 residues within 4Å: Chain A: H.132, D.134, H.295, R.310 Ligands: AKG.2 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.132, A:D.134, A:H.295, H2O.2, H2O.8, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jonnalagadda, R. et al., Biochemical and crystallographic investigations into isonitrile formation by a nonheme iron-dependent oxidase/decarboxylase. J.Biol.Chem. (2021)

Release Date

2021-01-06

Peptides

ScoE protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ScoE protein

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