SMTL ID : 3c9t.1

AaThiL complexed with AMPPCP and TMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.44, D.246 Ligands: TPS.6, ACP.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.246, A:D.246 MG.2: 4 residues within 4Å: Chain A: D.79, D.107 Ligands: MG.4, ACP.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.79, A:D.79, A:D.107 MG.3: 4 residues within 4Å: Chain A: D.246, D.251, H.254 Ligands: ACP.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.246, A:D.251, A:H.254 MG.4: 5 residues within 4Å: Chain A: D.63, D.107, D.243 Ligands: MG.2, ACP.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.63, A:D.107, A:D.243 MG.5: 4 residues within 4Å: Chain A: N.155 Chain B: D.79 Ligands: ACP.7, TPS.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.79 MG.8: 4 residues within 4Å: Chain A: D.79 Chain B: N.155 Ligands: TPS.6, ACP.13 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: D.246 Ligands: ACP.7, TPS.14 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.246, B:D.246 MG.10: 6 residues within 4Å: Chain B: D.63, D.107, D.243, S.245 Ligands: ACP.7, MG.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.63, B:D.107, B:D.243 MG.11: 5 residues within 4Å: Chain B: D.79, V.103, D.107 Ligands: ACP.7, MG.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.79, B:D.107 MG.12: 3 residues within 4Å: Chain B: D.246, D.251, H.254 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.246, B:D.251

2 x TPS: THIAMIN PHOSPHATE(Non-covalent)

TPS.6: 15 residues within 4Å: Chain A: D.79, G.84, V.85, H.86, L.200, H.221, S.245, D.246, E.296, Y.298, W.339, H.341 Ligands: MG.1, MG.8, ACP.13 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.200, A:W.339 Hydrogen bonds: A:H.86 Salt bridges: A:H.86, A:H.341 pi-Stacking: A:W.339, A:W.339 TPS.14: 15 residues within 4Å: Chain B: D.79, G.84, V.85, H.86, F.87, L.88, L.200, H.221, D.246, E.296, W.339, H.341 Ligands: MG.5, ACP.7, MG.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.88, B:L.200, B:W.339 Hydrogen bonds: B:E.296, B:Y.298 Salt bridges: B:H.86, B:H.341 pi-Stacking: B:W.339, B:W.339

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.7: 25 residues within 4Å: Chain A: I.120, L.122, Y.137, G.153, G.154, N.155, I.156 Chain B: E.44, I.48, I.51, I.60, G.61, D.62, D.63, D.79, D.107, R.178, S.245, D.246, H.254 Ligands: MG.5, MG.9, MG.10, MG.11, TPS.14 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.61, B:D.62, B:D.62, B:D.79, B:S.245, B:D.246, A:Y.137, A:Y.137, A:G.154, A:N.155 Water bridges: B:T.78 Salt bridges: B:R.178, B:H.254 ACP.13: 25 residues within 4Å: Chain A: I.48, I.51, I.60, G.61, D.62, D.63, D.79, D.107, R.178, S.245, D.246, H.254 Chain B: I.120, L.122, Y.137, G.153, G.154, N.155, I.156 Ligands: MG.1, MG.2, MG.3, MG.4, TPS.6, MG.8 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:Y.137, B:Y.137, B:G.154, B:N.155, B:N.155, A:G.61, A:D.62, A:D.62, A:S.245, A:D.246 Water bridges: A:D.79, A:D.107 Salt bridges: A:R.178, A:H.254

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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