SMTL ID : 6mfm.1

Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP) and thiamine diphosphate (TPP), orthorhombic crystal form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 21 residues within 4Å: Chain A: D.51, G.56, R.57, H.58, F.59, P.60, L.173, L.184, S.208, D.209, G.254, D.256, Y.258, Y.309, H.311 Chain B: D.126 Ligands: MG.2, MG.3, MG.5, ADP.10, NA.11 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.173, A:Y.309, A:Y.309 Hydrogen bonds: A:S.208, A:D.256 Water bridges: A:T.52, A:K.71, A:K.71, A:Y.258 Salt bridges: A:H.58, A:H.311 pi-Stacking: A:Y.309 TPP.13: 21 residues within 4Å: Chain A: D.126 Chain B: D.51, G.56, R.57, H.58, F.59, P.60, L.173, L.184, S.208, D.209, G.254, D.256, Y.258, Y.309, H.311 Ligands: ADP.6, NA.7, MG.8, MG.14, MG.15 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.173, B:Y.309, B:Y.309 Hydrogen bonds: B:S.208, B:D.256 Water bridges: B:K.71, B:K.71, B:Y.258, B:Y.258 Salt bridges: B:H.58, B:H.311 pi-Stacking: B:Y.309

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.51, D.79 Ligands: TPP.1, MG.4, MG.5, ADP.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.51, A:D.79, H2O.2, H2O.6 MG.3: 2 residues within 4Å: Chain A: D.209 Ligands: TPP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.209, A:D.209, H2O.11, H2O.11, H2O.12 MG.4: 6 residues within 4Å: Chain A: D.79, R.151, D.206 Chain B: D.34 Ligands: MG.2, ADP.10 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.34, A:D.79, A:D.206, H2O.2, H2O.6 MG.5: 7 residues within 4Å: Chain A: D.51 Chain B: D.126 Ligands: TPP.1, MG.2, NA.9, ADP.10, NA.11 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.51, B:D.126, H2O.13 MG.8: 7 residues within 4Å: Chain A: D.126 Chain B: D.51 Ligands: ADP.6, NA.7, NA.12, TPP.13, MG.14 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.51, A:D.126, H2O.5 MG.14: 6 residues within 4Å: Chain B: D.51, D.79 Ligands: ADP.6, MG.8, TPP.13, MG.16 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.51, B:D.79, H2O.13, H2O.15 MG.15: 3 residues within 4Å: Chain B: D.209 Ligands: ADP.6, TPP.13 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.209, H2O.1, H2O.4, H2O.11 MG.16: 6 residues within 4Å: Chain A: D.34 Chain B: D.79, R.151, D.206 Ligands: ADP.6, MG.14 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.79, B:D.206, A:D.34, H2O.15, H2O.15

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

ADP.6: 23 residues within 4Å: Chain A: E.11, F.12, I.15, F.19, I.31, G.32, D.33, D.34, L.92, G.124, G.125, D.126, T.127 Chain B: D.51, D.79, R.151, S.208 Ligands: MG.8, NA.12, TPP.13, MG.14, MG.15, MG.16 17 PLIP interactions: 8 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:G.32, A:D.33, A:D.33, A:D.34, A:G.125, A:T.127, B:D.51, B:S.208, B:S.208 Water bridges: A:G.125, A:T.127, B:R.151, B:R.151, B:R.151, B:R.151, B:R.151 Salt bridges: B:R.151 ADP.10: 22 residues within 4Å: Chain A: D.51, D.79, R.151, S.208 Chain B: E.11, F.12, I.15, F.19, I.31, G.32, D.33, D.34, L.92, G.124, G.125, D.126, T.127 Ligands: TPP.1, MG.2, MG.4, MG.5, NA.9 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:E.11, B:G.32, B:D.33, B:D.33, B:G.125, B:D.126, B:T.127, B:T.127, A:S.208, A:S.208 Water bridges: B:G.125, B:T.127, A:R.151, A:R.151, A:R.151, A:R.151, A:D.206 Salt bridges: A:R.151

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

NA.7: 6 residues within 4Å: Chain A: D.126, T.128 Chain B: D.51, T.52 Ligands: MG.8, TPP.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.58 NA.9: 7 residues within 4Å: Chain A: C.49, A.50, D.51, D.79 Chain B: G.125 Ligands: MG.5, ADP.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.50, A:D.79 NA.11: 7 residues within 4Å: Chain A: D.51, T.52, H.58 Chain B: D.126, T.128 Ligands: TPP.1, MG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.58 NA.12: 6 residues within 4Å: Chain A: G.125 Chain B: A.50, D.51, D.79 Ligands: ADP.6, MG.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.50, B:D.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sullivan, A.H. et al., Crystal structures of thiamine monophosphate kinase from Acinetobacter baumannii in complex with substrates and products. Sci Rep (2019)

Release Date

2018-09-26

Peptides

Thiamine-monophosphate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thiamine-monophosphate kinase

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