This entry has been superseded by
6MFM
on April 27, 2022, midnight.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-dimer
- Ligands
- 8 x NA: SODIUM ION(Non-functional Binders)
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 6 residues within 4Å:- Chain A: D.79, R.151, D.206
- Chain B: D.34
- Ligands: NA.1, ADP.9
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.2, H2O.6
MG.4: 7 residues within 4Å:- Chain A: D.51
- Chain B: D.126
- Ligands: NA.1, NA.8, ADP.9, TPP.12, NA.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.13
MG.7: 7 residues within 4Å:- Chain A: D.126
- Chain B: D.51
- Ligands: ADP.5, NA.6, TPP.10, NA.14, NA.15
3 PLIP interactions:1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: A:D.126, B:D.51, H2O.6
MG.11: 6 residues within 4Å:- Chain A: D.34
- Chain B: D.79, R.151, D.206
- Ligands: ADP.5, NA.15
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.16
- 2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.5: 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.7, TPP.10, MG.11, NA.14, NA.15, NA.16
17 PLIP interactions:9 interactions with chain A, 8 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.79, B:S.208
- Water bridges: A:G.125, A:D.126, A:T.127, B:R.151, B:R.151, B:R.151, B:R.151, B:R.151
- Salt bridges: B:R.151
ADP.9: 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: NA.1, MG.3, MG.4, NA.8, TPP.12
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
- 2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)
TPP.10: 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.5, NA.6, MG.7, NA.15, NA.16
14 PLIP interactions:14 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:D.209, B:D.209, B:Y.258, B:Y.258
- Salt bridges: B:H.58, B:H.311
- pi-Stacking: B:Y.309
TPP.12: 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: NA.1, NA.2, MG.4, ADP.9, NA.13
13 PLIP interactions:13 interactions with chain A- Hydrophobic interactions: A:L.173, A:Y.309, A:Y.309
- Hydrogen bonds: A:S.208, 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
- 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
AB
B