SMTL ID : 8yks.1 (1 other biounit)

PaThiL in complex with AMP-PNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.97, R.168, D.233 Chain B: D.52 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.52, A:D.97, A:D.233, H2O.1, H2O.2, H2O.3 MG.2: 4 residues within 4Å: Chain A: D.69, D.97 Ligands: NA.5, ANP.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.69, A:D.69, A:D.97, H2O.3, H2O.5 MG.3: 3 residues within 4Å: Chain B: D.144 Ligands: NA.4, ANP.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.144, H2O.5, H2O.10 MG.8: 4 residues within 4Å: Chain A: D.52 Chain B: D.97, R.168, D.233 6 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.52, B:D.97, B:D.233, H2O.11, H2O.11, H2O.12 MG.9: 4 residues within 4Å: Chain B: D.69, D.97 Ligands: NA.12, ANP.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.69, B:D.69, B:D.97, H2O.12, H2O.14 MG.10: 3 residues within 4Å: Chain A: D.144 Ligands: NA.11, ANP.13 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.144, H2O.1, H2O.14

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

NA.4: 4 residues within 4Å: Chain A: D.69 Chain B: D.144 Ligands: MG.3, ANP.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.69, A:D.69 NA.5: 4 residues within 4Å: Chain A: S.67, D.97 Chain B: D.52 Ligands: MG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.97 Water bridges: A:T.68 NA.11: 4 residues within 4Å: Chain A: D.144 Chain B: D.69 Ligands: MG.10, ANP.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.69 NA.12: 4 residues within 4Å: Chain A: D.52 Chain B: S.67, D.97 Ligands: MG.9 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.52 Water bridges: B:T.68

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

ANP.6: 18 residues within 4Å: Chain A: D.69, D.97, S.235, D.236 Chain B: R.30, F.33, I.49, G.50, D.51, L.110, L.140, G.142, G.143, D.144, T.145 Ligands: MG.2, MG.3, NA.4 21 PLIP interactions: 14 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:R.30, B:G.50, B:D.51, B:D.51, B:G.143, B:D.144, B:T.145, B:T.145, A:D.69, A:S.235, A:S.235, A:D.236 Water bridges: B:D.51, B:D.52, B:D.52, B:G.143, B:T.145, B:T.145, A:R.168, A:R.168, A:R.168 ANP.13: 18 residues within 4Å: Chain A: R.30, F.33, I.49, G.50, D.51, L.110, L.140, G.142, G.143, D.144, T.145 Chain B: D.69, D.97, S.235, D.236 Ligands: MG.9, MG.10, NA.11 20 PLIP interactions: 7 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:D.69, B:S.235, B:S.235, B:D.236, A:R.30, A:G.50, A:D.51, A:D.51, A:G.143, A:T.145 Water bridges: B:R.168, B:R.168, B:R.168, A:E.27, A:D.51, A:D.52, A:D.52, A:G.143, A:T.145, A:T.145

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: S.22, M.23, G.24, E.25, F.26, E.27 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.24, A:G.24, A:F.26, A:E.27 Water bridges: A:Q.21, A:E.25, A:R.147 GOL.14: 6 residues within 4Å: Chain B: S.22, M.23, G.24, E.25, F.26, E.27 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.24, B:G.24, B:F.26, B:E.27 Water bridges: B:Q.21, B:E.25, B:E.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, J.Q. et al., ThiL in complex with AMP-PNP. To Be Published

Release Date

2025-03-12

Peptides

Thiamine-monophosphate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Thiamine-monophosphate kinase

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