SMTL ID : 5cc8.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 21 residues within 4Å: Chain A: 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, D.206, S.208, D.209 Ligands: MG.6, MG.10, K.12, MG.14 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:D.79, 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:D.209, B:D.209, A:G.125, A:T.127 ANP.13: 21 residues within 4Å: Chain A: D.51, D.79, R.151, S.208, D.209 Chain B: I.15, F.19, I.31, G.32, D.33, D.34, L.92, L.122, G.124, G.125, D.126, T.127 Ligands: MG.2, MG.4, MG.5, K.8 15 PLIP interactions: 9 interactions with chain B, 6 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:R.151, A:S.208 Water bridges: B:D.34, B:G.125, B:T.127, A:R.151, A:D.209, A:D.209, A:D.209

6 x MG: MAGNESIUM ION(Non-covalent)

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

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

CL.3: 3 residues within 4Å: Chain A: T.128, Q.129 Chain B: R.57 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: R.57, H.58 Chain B: T.128, Q.129 Ligand excluded by PLIP

4 x K: POTASSIUM ION(Non-covalent)

K.7: 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: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:A.82, A:V.149, A:M.204, B:D.33, B:D.34 K.8: 7 residues within 4Å: Chain A: C.49, A.50, D.51, D.79 Chain B: D.34 Ligands: MG.4, ANP.13 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.34, H2O.2, H2O.5, H2O.8 K.11: 8 residues within 4Å: Chain A: D.33, D.34 Chain B: A.82, M.83, V.149, L.150, R.151, M.204 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:D.33, A:D.34, B:A.82, B:V.149, B:M.204 K.12: 6 residues within 4Å: Chain A: D.34 Chain B: C.49, A.50, D.79 Ligands: ANP.1, MG.14 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.34, H2O.13, H2O.16, H2O.18

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

2015-09-02

Peptides

Thiamine-monophosphate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thiamine-monophosphate kinase

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