SMTL ID : 6fd2.1 (1 other biounit)

Radical SAM 1,2-diol dehydratase AprD4 in complex with its substrate paromamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

1 x D5E: paromamine(Non-covalent)

D5E.1: 14 residues within 4Å: Chain A: Y.26, A.27, T.32, E.37, F.39, Y.216, R.250, E.280, E.303, L.344, N.375, S.377, S.406 Ligands: 5AD.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.27, A:T.32, A:D.38, A:Y.216, A:Y.216, A:R.250, A:E.280, A:E.303, A:E.303, A:N.375, A:S.406, A:S.406

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 12 residues within 4Å: Chain A: C.206, Y.208, C.210, R.211, C.214, Y.216, P.217, P.252, R.282, K.320 Ligands: MET.3, 5AD.4 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain A Metal complexes: MET.3, A:C.206, A:C.210, A:C.214 Salt bridges: A:E.307

1 x MET: METHIONINE(Non-covalent)

MET.3: 7 residues within 4Å: Chain A: P.252, T.281, R.282, G.305, K.320 Ligands: SF4.2, 5AD.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.252, A:T.281, A:G.305 Salt bridges: A:R.282, A:K.320

1 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.4: 16 residues within 4Å: Chain A: Y.213, C.214, P.215, Y.216, E.307, L.344, L.346, S.377, V.378, I.379, T.380, Y.382, S.406 Ligands: D5E.1, SF4.2, MET.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.216 Hydrogen bonds: A:Y.213, A:E.307, A:S.377, A:T.380

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, W.Q. et al., 1,2-Diol Dehydration by the Radical SAM Enzyme AprD4: A Matter of Proton Circulation and Substrate Flexibility. J. Am. Chem. Soc. (2018)

Release Date

2018-01-17

Peptides

Putative apramycin biosynthetic oxidoreductase 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Putative apramycin biosynthetic oxidoreductase 4

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