SMTL ID : 5dd7.1

Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with AMPPNP and thiamine-monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 27 residues within 4Å: Chain A: E.11, F.12, I.15, F.19, I.31, G.32, D.33, D.34, L.92, I.94, G.124, G.125, D.126, T.127 Chain B: D.51, D.79, R.151, D.206, S.208, D.209 Ligands: MG.3, K.6, TPS.12, MG.13, MG.14, K.15, MG.17 15 PLIP interactions: 6 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:D.51, B:R.151, B:S.208, A:G.32, A:D.33, A:D.33, A:D.34, A:G.125, A:T.127 Water bridges: B:R.151, B:R.151, B:D.209, A:D.34, A:G.125, A:T.127 ANP.16: 26 residues within 4Å: Chain A: D.51, D.79, R.151, S.208, D.209 Chain B: E.11, F.12, I.15, F.19, I.31, G.32, D.33, D.34, L.92, I.94, G.124, G.125, D.126, T.127 Ligands: MG.2, K.4, TPS.8, MG.9, MG.10, MG.11, K.19 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:G.32, B:D.33, B:D.33, B:G.125, B:T.127, B:T.127, A:D.51, A:R.151, A:S.208 Water bridges: B:E.11, B:E.11, B:D.34, B:G.125, A:R.151, A:R.151, A:D.209, A:D.209, A:D.209

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.209 Ligands: TPS.8, ANP.16, K.19 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.209, A:D.209, H2O.11, H2O.13 MG.3: 5 residues within 4Å: Chain A: D.126 Chain B: D.51 Ligands: ANP.1, K.6, MG.13 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.2 MG.9: 6 residues within 4Å: Chain A: D.51, D.79 Ligands: K.4, MG.10, MG.11, ANP.16 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.51, A:D.79, H2O.4, H2O.13 MG.10: 6 residues within 4Å: Chain A: D.79, R.151, D.206 Chain B: D.34 Ligands: MG.9, ANP.16 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.79, A:D.206, B:D.34, H2O.5, H2O.13 MG.11: 5 residues within 4Å: Chain A: D.51 Chain B: D.126 Ligands: MG.9, ANP.16, K.19 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.2 MG.13: 6 residues within 4Å: Chain B: D.51, D.79 Ligands: ANP.1, MG.3, MG.14, K.15 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.51, B:D.79, H2O.13, H2O.14 MG.14: 6 residues within 4Å: Chain A: D.34 Chain B: D.79, R.151, D.206 Ligands: ANP.1, MG.13 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.13, H2O.15 MG.17: 4 residues within 4Å: Chain B: D.209 Ligands: ANP.1, K.6, TPS.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.209, B:D.209, H2O.1, H2O.4

6 x K: POTASSIUM ION(Non-covalent)

K.4: 7 residues within 4Å: Chain A: C.49, A.50, D.51, D.79 Chain B: D.34 Ligands: MG.9, ANP.16 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.34, A:D.79, H2O.2, H2O.4, H2O.7 K.5: 8 residues within 4Å: Chain A: A.82, M.83, V.149, L.150, R.151, M.204 Chain B: D.33, D.34 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:D.33, B:D.34, A:A.82, A:V.149, A:M.204 K.6: 8 residues within 4Å: Chain A: E.11, D.126, T.127 Chain B: H.311 Ligands: ANP.1, MG.3, TPS.12, MG.17 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.11, A:D.126, A:T.127 K.15: 6 residues within 4Å: Chain A: D.34 Chain B: C.49, D.51, D.79 Ligands: ANP.1, MG.13 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.79, A:D.34, H2O.2, H2O.15, H2O.17 K.18: 6 residues within 4Å: Chain A: D.33, D.34 Chain B: A.82, M.83, V.149, M.204 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:A.82, B:V.149, B:M.204, A:D.33, A:D.34 K.19: 8 residues within 4Å: Chain A: H.311 Chain B: E.11, D.126, T.127 Ligands: MG.2, TPS.8, MG.11, ANP.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.11, B:D.126, B:T.127

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 4 residues within 4Å: Chain A: G.164, Q.165, R.183, R.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.190 Water bridges: A:R.190 EDO.20: 4 residues within 4Å: Chain B: G.164, Q.165, R.183, R.190 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.190 Water bridges: B:R.190, B:R.190

2 x TPS: THIAMIN PHOSPHATE(Non-covalent)

TPS.8: 20 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, G.255, D.256, Y.258, Y.309, H.311 Chain B: T.128 Ligands: MG.2, ANP.16, K.19 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.173, A:Y.309, A:Y.309 Hydrogen bonds: A:D.256 Water bridges: A:T.52, A:K.71, A:K.71, B:D.126 Salt bridges: A:H.58, A:H.311 pi-Stacking: A:Y.309 TPS.12: 19 residues within 4Å: Chain A: T.128 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: ANP.1, K.6, MG.17 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.173, B:Y.309, B:Y.309 Hydrogen bonds: B:D.256 Water bridges: B:D.51, 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

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

2015-09-16

Peptides

Thiamine-monophosphate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thiamine-monophosphate kinase