SMTL ID : 3c9u.1

AaThiL complexed with ADP and TPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.63, D.107, R.178, D.243 Ligands: MG.5, ADP.13 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.63, A:D.107, A:D.243, H2O.1 MG.2: 4 residues within 4Å: Chain A: D.63, T.77, D.107 Ligands: ADP.13 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.63, A:T.77, A:D.107, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.79 Chain B: N.155 Ligands: MG.5, TPP.7, ADP.13 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.79, H2O.1 MG.4: 2 residues within 4Å: Chain A: D.246 Ligands: TPP.7 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.246, A:D.246, H2O.1, H2O.8, H2O.16 MG.5: 6 residues within 4Å: Chain A: D.79, D.107 Ligands: MG.1, MG.3, TPP.7, ADP.13 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.79, A:D.107, A:D.107, H2O.1, H2O.1 MG.6: 5 residues within 4Å: Chain A: N.155 Chain B: D.79 Ligands: ADP.8, MG.11, TPP.14 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.79, H2O.12 MG.9: 4 residues within 4Å: Chain B: D.63, T.77, D.107 Ligands: ADP.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.63, B:T.77, B:D.107, H2O.12, H2O.12 MG.10: 2 residues within 4Å: Chain B: D.246 Ligands: TPP.14 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.246, B:D.246, H2O.15, H2O.16, H2O.16 MG.11: 6 residues within 4Å: Chain B: D.79, D.107 Ligands: MG.6, ADP.8, MG.12, TPP.14 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.79, B:D.107, B:D.107, H2O.12, H2O.12 MG.12: 6 residues within 4Å: Chain B: D.63, D.107, R.178, D.243 Ligands: ADP.8, MG.11 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.63, B:D.107, B:D.243, H2O.12, H2O.12

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.7: 16 residues within 4Å: Chain A: D.79, V.85, H.86, F.87, L.200, H.221, S.245, D.246, E.296, W.339, H.341 Chain B: N.155 Ligands: MG.3, MG.4, MG.5, ADP.13 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.200, A:W.339 Hydrogen bonds: A:S.245, A:E.296 Water bridges: A:E.296, A:H.341 Salt bridges: A:H.86, A:H.341 pi-Stacking: A:W.339, A:W.339 TPP.14: 17 residues within 4Å: Chain A: N.155 Chain B: D.79, G.84, V.85, H.86, F.87, L.200, H.221, S.245, D.246, E.296, W.339, H.341 Ligands: MG.6, ADP.8, MG.10, MG.11 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.200 Hydrogen bonds: B:D.79, B:S.245, B:E.296 Water bridges: B:Y.298, B:Y.298, B:Y.298, B:Y.298 Salt bridges: B:H.86, B:H.341 pi-Stacking: B:W.339, B:W.339

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

ADP.8: 22 residues within 4Å: Chain A: I.120, L.122, Y.137, G.153, G.154, N.155, I.156 Chain B: F.45, I.48, I.51, I.60, G.61, D.62, D.63, D.79, D.107, R.178 Ligands: MG.6, MG.9, MG.11, MG.12, TPP.14 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:G.61, B:D.62, B:D.62, B:D.63, A:Y.137, A:Y.137, A:G.154, A:N.155 Water bridges: B:T.77, B:T.77, B:R.178, B:R.178, B:D.243, B:S.245, A:G.154, A:I.156 Salt bridges: B:R.178 ADP.13: 22 residues within 4Å: Chain A: F.45, I.48, I.51, I.60, G.61, D.62, D.63, D.79, D.107, R.178 Chain B: I.120, L.122, Y.137, G.153, G.154, N.155, I.156 Ligands: MG.1, MG.2, MG.3, MG.5, TPP.7 19 PLIP interactions: 9 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:Y.137, B:Y.137, B:G.154, B:N.155, A:G.61, A:D.62, A:D.62 Water bridges: B:G.154, B:N.155, B:N.155, B:N.155, B:N.155, A:D.62, A:R.178, A:R.178, A:S.245, A:S.245, A:S.245 Salt bridges: A:R.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCulloch, K.M. et al., Structural studies of thiamin monophosphate kinase in complex with substrates and products. Biochemistry (2008)

Release Date

2008-03-18

Peptides

Thiamine monophosphate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thiamine monophosphate kinase

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