SMTL ID : 4s35.1

AMPPCP and TMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.1: 16 residues within 4Å: Chain A: I.8, D.9, G.10, S.11, G.12, K.13, T.14, T.15, R.90, R.139, E.147, G.176, E.177, E.178 Ligands: TMP.2, MG.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:D.9, A:G.10, A:G.12, A:K.13, A:K.13, A:K.13, A:T.14, A:T.14, A:T.15, A:T.15, A:R.90, A:R.90, A:R.139, A:G.176 Water bridges: A:R.139, A:R.139, A:R.139, A:R.139, A:E.178 pi-Cation interactions: A:R.139 ACP.6: 16 residues within 4Å: Chain B: I.8, D.9, G.10, S.11, G.12, K.13, T.14, T.15, R.90, R.139, E.147, G.176, E.177, E.178 Ligands: TMP.7, MG.8 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:D.9, B:G.10, B:S.11, B:G.12, B:K.13, B:K.13, B:K.13, B:T.14, B:T.15, B:T.15, B:R.90, B:R.90, B:E.147, B:G.176 Water bridges: B:T.14, B:T.14, B:T.14, B:R.139, B:R.139, B:R.139, B:R.139, B:E.178 pi-Cation interactions: B:R.139

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.2: 15 residues within 4Å: Chain A: D.9, E.36, P.37, R.47, F.64, R.68, R.90, S.94, T.95, Y.98, Q.99, N.144, F.146 Ligands: ACP.1, MG.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.36, A:Y.98 Hydrogen bonds: A:R.68, A:Q.99, A:Q.99, A:N.144, A:N.144 Water bridges: A:K.13, A:T.14, A:D.89, A:D.89, A:D.89 Salt bridges: A:R.47, A:R.90 pi-Stacking: A:F.64 TMP.7: 15 residues within 4Å: Chain B: D.9, E.36, P.37, R.47, F.64, R.68, R.90, S.94, T.95, Y.98, Q.99, N.144, F.146 Ligands: ACP.6, MG.8 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:E.36, B:Y.98 Hydrogen bonds: B:R.68, B:Q.99, B:Q.99, B:N.144, B:N.144 Water bridges: B:T.14, B:E.36, B:E.36, B:D.89, B:D.89 Salt bridges: B:R.47, B:R.90 pi-Stacking: B:F.64

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.14 Ligands: ACP.1, TMP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.14, H2O.1, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain A: Y.29, F.30, D.83 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.83 MG.8: 3 residues within 4Å: Chain B: T.14 Ligands: ACP.6, TMP.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.14, H2O.9, H2O.9, H2O.9 MG.9: 4 residues within 4Å: Chain B: P.132, V.133, E.153, R.156 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.153

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

EDO.5: 3 residues within 4Å: Chain A: D.134, I.135, R.138 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain B: K.19, E.179 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.19, B:K.19

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

CL.10: 2 residues within 4Å: Chain B: I.96, N.114 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biswas, A. et al., Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate. Febs J. (2017)

Release Date

2016-01-27

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate kinase

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