SMTL ID : 5k87.1

crystal structure of malonate bound to methylaconitate isomerase PrpF from Shewanella oneidensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-dimer

Ligands

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 8 residues within 4Å: Chain A: T.70, S.71, S.72, Q.242, K.317, L.318, H.319, H.320 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:K.317 Hydrogen bonds: A:S.71, A:S.72, A:S.72, A:Q.242, A:H.320 Water bridges: A:T.70, A:T.70 Salt bridges: A:H.319, A:H.320 MLI.2: 10 residues within 4Å: Chain A: S.24, S.72, E.75, C.109, G.110, N.111, H.319, M.323, G.324, T.325 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:M.323 Hydrogen bonds: A:S.24, A:G.110, A:N.111, A:N.111, A:G.324, A:T.325 Salt bridges: A:H.319 MLI.3: 8 residues within 4Å: Chain B: T.70, S.71, S.72, Q.242, K.317, L.318, H.319, H.320 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:K.317 Hydrogen bonds: B:S.71, B:S.71, B:S.72, B:S.72, B:Q.242, B:H.320 Water bridges: B:T.70, B:T.70 Salt bridges: B:H.319, B:H.320 MLI.4: 9 residues within 4Å: Chain B: S.24, E.75, C.109, G.110, N.111, H.319, M.323, G.324, T.325 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:M.323 Hydrogen bonds: B:S.24, B:G.110, B:N.111, B:N.111, B:G.324, B:T.325, B:T.325 Water bridges: B:T.325 Salt bridges: B:H.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rocco, C.J. et al., The PrpF protein of Shewanella oneidensis MR-1 catalyzes the isomerization of 2-methyl-cis-aconitate during the catabolism of propionate via the AcnD-dependent 2-methylcitric acid cycle. PLoS ONE (2017)

Release Date

2017-05-31

Peptides

2-methyl-aconitate isomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-methyl-aconitate isomerase