SMTL ID : 5tg0.1

Crystal structure of the dimethylsulfoniopropionate (DMSP) lyase DddK complexed with iron and zinc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 7 residues within 4Å: Chain A: H.76, H.78, E.82, Y.84, I.110, H.116 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.78, A:E.82, A:Y.84, A:H.116, H2O.1 FE.3: 7 residues within 4Å: Chain B: H.76, H.78, E.82, Y.84, I.110, H.116 Ligands: ZN.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.78, B:E.82, B:Y.84, B:H.116, H2O.8

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 8 residues within 4Å: Chain A: H.76, H.78, E.82, Y.84, H.116, F.132, Y.142 Ligands: FE.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.76, A:H.78, A:E.82, A:H.116, H2O.1 ZN.4: 8 residues within 4Å: Chain B: H.76, H.78, E.82, Y.84, H.116, F.132, Y.142 Ligands: FE.3 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.76, B:H.78, B:E.82, B:H.116, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schnicker, N.J. et al., Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter. Biochemistry (2017)

Release Date

2017-06-14

Peptides

dimethylsulfoniopropionate lyase DddK: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

dimethylsulfoniopropionate lyase DddK

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