SMTL ID : 6ter.1 (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

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: R.115, Q.116, G.118, D.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.115 GOL.2: 4 residues within 4Å: Chain A: R.209, D.272 Ligands: PEG.14, PEG.26 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.209 GOL.5: 2 residues within 4Å: Chain A: D.293, M.296 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.293 GOL.9: 5 residues within 4Å: Chain A: K.227, Y.228, A.318, Q.319, G.320 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.227, A:Y.228, A:Y.228 GOL.11: 10 residues within 4Å: Chain A: V.133, P.134, G.136, S.137, G.138, L.139, S.140, S.141 Ligands: PEG.4, PEG.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.138, A:L.139, A:S.140, A:S.141, A:S.141 GOL.13: 1 residues within 4Å: Ligands: PGE.21 No protein-ligand interaction detected (PLIP) GOL.16: 4 residues within 4Å: Chain A: R.414, E.415, A.416, K.417 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.414, A:E.415 GOL.23: 2 residues within 4Å: Ligands: PGE.19, PG4.22 No protein-ligand interaction detected (PLIP) GOL.25: 5 residues within 4Å: Chain A: G.320, D.321, I.322, K.323, Y.360 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.321, A:I.322, A:K.323

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

PEG.3: 5 residues within 4Å: Chain A: V.264, V.269, T.270, G.273, I.274 No protein-ligand interaction detected (PLIP) PEG.4: 9 residues within 4Å: Chain A: S.142, E.179, S.186, T.187, D.191 Ligands: GOL.11, PEG.12, GLA.27, GAL.28 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.142, A:E.179, A:D.191 Water bridges: A:E.179, A:G.367 PEG.6: 6 residues within 4Å: Chain A: V.16, T.20, A.30, V.34, A.416, L.418 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.20, A:T.20 PEG.7: 6 residues within 4Å: Chain A: Y.50, A.52, C.208, P.210, A.265, N.266 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.49, A:A.52, A:N.266 PEG.8: 2 residues within 4Å: Chain A: S.164, D.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.165 PEG.10: 2 residues within 4Å: Chain A: G.397, N.399 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.399 PEG.12: 13 residues within 4Å: Chain A: G.136, S.137, G.138, H.241, T.365, G.366, G.367, G.368, G.370, G.371, S.372 Ligands: PEG.4, GOL.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.136, A:G.368, A:S.372, A:S.372 Water bridges: A:G.367 PEG.14: 5 residues within 4Å: Chain A: D.272, S.275, R.311 Ligands: GOL.2, PEG.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.275, A:R.311 PEG.15: 6 residues within 4Å: Chain A: I.176, N.180, T.187, G.188, G.189, R.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.180, A:G.188, A:R.252, A:R.252 PEG.17: 2 residues within 4Å: Chain A: K.298, E.341 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.298, A:E.341 PEG.18: 5 residues within 4Å: Chain A: S.275, K.276, A.277, Q.280 Ligands: PEG.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.275, A:Q.280 PEG.26: 4 residues within 4Å: Chain A: G.273, K.276, A.277 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.276 Water bridges: A:D.278

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

PGE.19: 7 residues within 4Å: Chain A: V.87, A.88, E.89, A.90, V.100 Ligands: PG4.22, GOL.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.89 Water bridges: A:D.101 PGE.20: 5 residues within 4Å: Chain A: G.246, Q.247, A.249, Q.250, R.251 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.247, A:Q.250 Water bridges: A:Q.250, A:Q.250 PGE.21: 2 residues within 4Å: Chain A: Q.250 Ligands: GOL.13 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.22: 6 residues within 4Å: Chain A: R.71, R.77, V.87, E.89 Ligands: PGE.19, GOL.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.71, A:R.71, A:R.77 PG4.24: 4 residues within 4Å: Chain A: V.156, Y.157, G.158, G.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.156

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

GLA.27: 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.28 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:E.46, A:H.47, A:D.49, A:T.187, A:G.188, A:G.189, A:L.190, A:D.191, A:Y.248, A:G.367 Water bridges: A:R.40, A:T.48, A:D.191, A:Q.192, A:Q.192 Salt bridges: A:R.40

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

GAL.28: 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.27 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:E.46, A:H.47, A:D.49, A:T.187, A:G.188, A:G.189, A:L.190, A:Y.248 Water bridges: A:R.40, A:T.48, A:D.191, A:Q.192, A:Q.192

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

CL.29: 2 residues within 4Å: Chain A: A.83, D.85 Ligand excluded by PLIP

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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