SMTL ID : 6tep.1 (3 other biounits)

Crystal structure of a galactokinase from Bifidobacterium infantis in complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 6 residues within 4Å: Chain A: K.69, P.70, R.71, E.72, D.73, D.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.69, A:E.72, A:D.73, A:D.73

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: G.320, D.321, I.322, K.323, Y.360 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.321, A:I.322, A:K.323, A:Y.360 Water bridges: A:G.320, A:A.324 GOL.3: 8 residues within 4Å: Chain A: E.46, H.47, T.48, D.49, Y.50, L.190, Y.248, G.366 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.46, A:E.46, A:H.47, A:T.48, A:D.49, A:Y.248

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 16 residues within 4Å: Chain A: S.80, V.82, W.103, Y.106, S.131, P.134, L.135, G.136, S.137, G.138, L.139, S.140, S.141, S.142, M.145 Ligands: MG.7 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.80, A:S.80, A:G.136, A:S.137, A:G.138, A:L.139, A:S.140, A:S.141, A:S.142, A:S.142 Water bridges: A:G.81, A:V.82, A:Y.106, A:Y.106, A:S.131, A:G.138, A:S.140, A:D.191

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: Q.250, R.251, T.254, R.299 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: T.74, D.93, R.115 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain A: S.142 Ligands: ADP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.142, H2O.2, H2O.4, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keenan, T. et al., Profiling Substrate Promiscuity of Wild-Type Sugar Kinases for Multi-fluorinated Monosaccharides. Cell Chem Biol (2020)

Release Date

2020-06-10

Peptides

Galactokinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Galactokinase

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