SMTL ID : 8sut.1

Crystal structure of YisK from Bacillus subtilis in complex with reaction product 4-Hydroxy-2-oxoglutaric acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x IO9: (2~{R})-2-oxidanyl-4-oxidanylidene-pentanedioic acid(Non-covalent)

IO9.1: 16 residues within 4Å: Chain A: I.100, G.101, K.102, H.107, M.111, F.124, E.151, E.153, D.182, R.186, Q.189, F.195, K.199, G.268, T.269 Ligands: MN.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.102, A:R.186, A:Q.189, A:Q.189, A:K.199, A:T.269 Water bridges: A:N.103, A:G.268 Salt bridges: A:K.102, A:H.107, A:H.107, A:R.186 IO9.4: 16 residues within 4Å: Chain B: I.100, G.101, K.102, H.107, M.111, F.124, E.151, E.153, D.182, R.186, Q.189, F.195, K.199, G.268, T.269 Ligands: MN.3 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.102, B:R.186, B:Q.189, B:Q.189, B:Q.189, B:K.199, B:T.269 Water bridges: B:G.268 Salt bridges: B:K.102, B:H.107, B:R.186, B:K.199

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: I.100, E.151, E.153, D.182, K.199 Ligands: IO9.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.151, A:E.153, A:D.182, H2O.1 MN.3: 6 residues within 4Å: Chain B: I.100, E.151, E.153, D.182, K.199 Ligands: IO9.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.151, B:E.153, B:D.182, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, T. et al., Bacillus subtilis YisK possesses oxaloacetate decarboxylase activity and exhibits Mbl-dependent localization. J.Bacteriol. (2024)

Release Date

2023-11-01

Peptides

Fumarylacetoacetate hydrolase family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fumarylacetoacetate hydrolase family protein

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