SMTL ID : 8yku.1

PaThiL in complex with AMP-PNP and TMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 1 residues within 4Å: Chain B: Q.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.63, B:G.163 Water bridges: B:A.165 ACT.15: 2 residues within 4Å: Chain A: Q.116, W.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.116 ACT.18: 1 residues within 4Å: Chain A: Q.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.63, A:G.163 Water bridges: A:A.165 ACT.32: 2 residues within 4Å: Chain B: Q.116, W.121 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.116

16 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: E.202, E.205 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.202, A:E.202, A:E.205, A:E.205 CA.3: 4 residues within 4Å: Chain A: S.67, D.97 Chain B: D.52 Ligands: ANP.11 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:S.67, B:D.52, H2O.3, H2O.9, H2O.10 CA.4: 4 residues within 4Å: Chain A: D.69 Chain B: D.144 Ligands: CA.5, ANP.11 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.69, B:D.144, H2O.1, H2O.1, H2O.6 CA.5: 4 residues within 4Å: Chain A: D.69, D.97 Ligands: CA.4, ANP.11 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.69, A:D.97, H2O.2, H2O.3, H2O.6 CA.6: 5 residues within 4Å: Chain A: D.97, R.168, D.233 Chain B: D.52 Ligands: ANP.11 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.97, A:D.233, B:D.52, H2O.1 CA.7: 2 residues within 4Å: Chain A: D.236 Ligands: TPS.10 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.236, H2O.2, H2O.7, H2O.7, H2O.12 CA.8: 3 residues within 4Å: Chain A: D.236, D.241, H.244 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.236, A:D.241, A:H.244, H2O.1, H2O.3, H2O.7 CA.9: 6 residues within 4Å: Chain A: A.100, M.101, L.166, A.231 Chain B: D.51, D.52 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:D.51, B:D.52, A:A.100, A:L.166, A:A.231 CA.19: 2 residues within 4Å: Chain B: E.202, E.205 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.202, B:E.202, B:E.205, B:E.205 CA.20: 4 residues within 4Å: Chain A: D.52 Chain B: S.67, D.97 Ligands: ANP.28 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:S.67, A:D.52, H2O.2, H2O.2, H2O.11 CA.21: 4 residues within 4Å: Chain A: D.144 Chain B: D.69 Ligands: CA.22, ANP.28 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.144, B:D.69, H2O.8, H2O.9, H2O.14 CA.22: 4 residues within 4Å: Chain B: D.69, D.97 Ligands: CA.21, ANP.28 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.69, B:D.97, H2O.10, H2O.11, H2O.14 CA.23: 5 residues within 4Å: Chain A: D.52 Chain B: D.97, R.168, D.233 Ligands: ANP.28 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.97, B:D.233, A:D.52, H2O.9 CA.24: 2 residues within 4Å: Chain B: D.236 Ligands: TPS.27 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.236, H2O.4, H2O.10, H2O.15, H2O.15 CA.25: 3 residues within 4Å: Chain B: D.236, D.241, H.244 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.236, B:D.241, B:H.244, H2O.9, H2O.11, H2O.15 CA.26: 6 residues within 4Å: Chain A: D.51, D.52 Chain B: A.100, M.101, L.166, A.231 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:D.51, A:D.52, B:A.100, B:L.166, B:A.231

2 x TPS: THIAMIN PHOSPHATE(Non-covalent)

TPS.10: 13 residues within 4Å: Chain A: V.75, H.76, F.77, P.78, R.89, L.190, Y.211, S.235, D.236, A.282, D.284 Chain B: T.146 Ligands: CA.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.190 Salt bridges: A:H.76 Water bridges: B:R.147 TPS.27: 13 residues within 4Å: Chain A: T.146 Chain B: V.75, H.76, F.77, P.78, R.89, L.190, Y.211, S.235, D.236, A.282, D.284 Ligands: CA.24 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.190 Hydrogen bonds: B:Y.211 Water bridges: B:Y.286, A:R.147 Salt bridges: B:H.76

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

ANP.11: 24 residues within 4Å: Chain A: D.69, D.97, R.168, D.233, S.235, D.236, H.244 Chain B: F.26, I.29, F.33, I.49, G.50, D.51, D.52, L.110, L.140, G.142, G.143, D.144, T.145 Ligands: CA.3, CA.4, CA.5, CA.6 23 PLIP interactions: 11 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:G.50, B:D.51, B:G.143, B:T.145, B:T.145, A:R.168, A:S.235 Water bridges: B:D.51, B:G.143, B:D.144, B:D.144, B:D.144, B:D.144, A:D.69, A:D.69, A:D.69, A:D.97, A:R.168, A:S.235, A:S.235, A:H.244 Salt bridges: A:R.168, A:H.244 ANP.28: 24 residues within 4Å: Chain A: F.26, I.29, F.33, I.49, G.50, D.51, D.52, L.110, L.140, G.142, G.143, D.144, T.145 Chain B: D.69, D.97, R.168, D.233, S.235, D.236, H.244 Ligands: CA.20, CA.21, CA.22, CA.23 21 PLIP interactions: 9 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:G.50, A:D.51, A:D.52, A:G.143, A:T.145, B:R.168, B:S.235 Water bridges: A:D.51, A:G.143, A:D.144, A:T.145, B:D.69, B:D.69, B:D.69, B:D.97, B:R.168, B:S.235, B:S.235, B:H.244 Salt bridges: B:R.168, B:H.244

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

PG4.12: 5 residues within 4Å: Chain A: M.132, Q.135, T.213, A.215, P.216 No protein-ligand interaction detected (PLIP) PG4.16: 6 residues within 4Å: Chain A: A.223, R.225, G.226, K.227, Y.296, E.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.223, A:G.226, A:K.227 PG4.29: 5 residues within 4Å: Chain B: M.132, Q.135, T.213, A.215, P.216 No protein-ligand interaction detected (PLIP) PG4.33: 6 residues within 4Å: Chain B: A.223, R.225, G.226, K.227, Y.296, E.299 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.223, B:G.226, B:K.227

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 5 residues within 4Å: Chain A: P.105, Q.135, C.136, G.137, F.218 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.134 PEG.30: 5 residues within 4Å: Chain B: P.105, Q.135, C.136, G.137, F.218 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.134

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

EDO.14: 4 residues within 4Å: Chain A: S.267, G.268, L.269, A.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.267 EDO.17: 1 residues within 4Å: Chain A: E.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.205 EDO.31: 4 residues within 4Å: Chain B: S.267, G.268, L.269, A.271 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.267 EDO.34: 1 residues within 4Å: Chain B: E.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.205

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

2024-08-07

Peptides

Thiamine-monophosphate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thiamine-monophosphate kinase

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