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

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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.69 NA.5: 4 residues within 4Å: Chain A: S.67, D.97 Chain B: D.52 Ligands: MG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.97 Water bridges: A:T.68 NA.12: 4 residues within 4Å: Chain A: D.144 Chain B: D.69 Ligands: MG.11, ANP.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.69, B:D.69 NA.13: 4 residues within 4Å: Chain A: D.52 Chain B: S.67, D.97 Ligands: MG.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.97 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.1, MG.3, NA.4 20 PLIP interactions: 8 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:D.69, A:S.235, A:S.235, A:D.236, B:R.30, B:G.50, B:D.51, B:G.143, B:T.145 Water bridges: A:T.70, A:R.168, A:R.168, A:R.168, B:D.51, B:D.52, B:D.52, B:D.52, B:G.143, B:T.145, B:T.145 ANP.14: 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.11, NA.12 20 PLIP interactions: 8 interactions with chain B, 12 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:G.143, A:T.145, A:T.145 Water bridges: B:T.70, B:R.168, B:R.168, B:R.168, A:D.51, A:D.52, A:D.52, A:G.143, A:T.145, A:T.145

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 3 residues within 4Å: Chain A: L.28, R.31, F.32 No protein-ligand interaction detected (PLIP) PG4.15: 3 residues within 4Å: Chain B: L.28, R.31, F.32 No protein-ligand interaction detected (PLIP)

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

EDO.8: 5 residues within 4Å: Chain A: V.75, H.76, F.77, P.78, Y.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.211, A:Y.211 EDO.16: 5 residues within 4Å: Chain B: V.75, H.76, F.77, P.78, Y.211 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.211

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
A

B
A

Thiamine-monophosphate kinase

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