SMTL ID : 6ter.2 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: A.271, D.272, S.275, V.304, T.305, I.307, E.308, R.311 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.272, A:S.275, A:I.307, A:E.308, A:R.311, A:R.311 GOL.6: 5 residues within 4Å: Chain A: E.32, K.69, P.70, E.72 Ligands: PEG.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.32, A:E.72 GOL.7: 3 residues within 4Å: Chain A: Q.238, N.399, A.400 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.400 GOL.9: 3 residues within 4Å: Chain A: E.8, T.11, E.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.14 GOL.10: 11 residues within 4Å: Chain A: S.137, G.138, L.347, M.364, T.365, G.366, G.367, G.368, G.370, G.371, S.372 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.138, A:G.367, A:G.368, A:S.372 GOL.12: 2 residues within 4Å: Chain A: D.93, G.94 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.93 GOL.17: 2 residues within 4Å: Chain A: E.394, K.395 No protein-ligand interaction detected (PLIP)

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

PEG.2: 5 residues within 4Å: Chain A: E.72, K.121, K.123, Y.157 Ligands: PEG.15 No protein-ligand interaction detected (PLIP) PEG.3: 3 residues within 4Å: Chain A: V.82, S.131, L.135 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.131 PEG.4: 10 residues within 4Å: Chain A: S.140, S.141, S.142, A.143, E.179, T.187, D.191, Q.192 Ligands: GLA.18, GAL.19 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.141, A:S.141, A:S.142, A:S.142, A:T.187, A:Q.192 Water bridges: A:G.136, A:E.179, A:D.191 PEG.5: 6 residues within 4Å: Chain A: W.35, D.154, D.155, G.158, D.163, R.414 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.155, A:R.414 Water bridges: A:G.160, A:R.414 PEG.8: 5 residues within 4Å: Chain A: S.275, K.276, A.277, D.278, Q.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.275, A:Q.280 PEG.11: 1 residues within 4Å: Chain A: E.72 No protein-ligand interaction detected (PLIP) PEG.13: 4 residues within 4Å: Chain A: V.87, A.88, E.89 Ligands: PEG.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.87, A:E.89 PEG.15: 5 residues within 4Å: Chain A: E.72, V.156, Y.157 Ligands: PEG.2, GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.156 PEG.16: 4 residues within 4Å: Chain A: E.89, G.99, V.100 Ligands: PEG.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.99

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.14: 2 residues within 4Å: Chain A: R.355, A.359 No protein-ligand interaction detected (PLIP)

1 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.18: 15 residues within 4Å: Chain A: R.40, E.46, H.47, D.49, Y.50, T.187, G.188, G.189, L.190, D.191, Y.248, G.366, G.367 Ligands: PEG.4, GAL.19 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:H.47, A:D.49, A:T.187, A:G.188, A:G.189, A:L.190, A:D.191 Water bridges: A:T.48, A:D.191, A:G.367 Salt bridges: A:R.40

1 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.19: 14 residues within 4Å: Chain A: E.46, H.47, D.49, Y.50, T.187, G.188, G.189, L.190, D.191, Y.248, G.366, G.367 Ligands: PEG.4, GLA.18 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.47, A:D.49, A:T.187, A:G.188, A:G.189, A:L.190 Water bridges: A:R.40, A:T.48, A:D.191

3 x NA: SODIUM ION(Non-functional Binders)

NA.20: 2 residues within 4Å: Chain A: F.6, E.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.6 NA.21: 4 residues within 4Å: Chain A: G.136, S.137, D.236, Q.238 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.136, A:Q.238, A:Q.238 NA.22: 2 residues within 4Å: Chain A: H.12, E.415 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.415

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
B

Galactokinase

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