SMTL ID : 5zax.1

Crystal structure of thymidylate kinase in complex with ADP, TDP and TMP from thermus thermophilus HB8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-dimer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 14 residues within 4Å: Chain A: L.11, D.12, G.13, S.14, G.15, K.16, T.17, T.18, A.178, L.180, P.181, E.182, I.185 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.13, A:S.14, A:G.15, A:K.16, A:T.17, A:T.18, A:T.18, A:L.180 Water bridges: A:K.16, A:T.17 Salt bridges: A:K.16

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.7, E.9, Y.92, D.94, T.127 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.7, A:D.94 MG.3: 5 residues within 4Å: Chain A: Y.62, S.66, R.69, L.93, A.115 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Y.62, A:S.66 MG.4: 3 residues within 4Å: Chain A: E.160, L.163, A.164 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: L.165, A.168, E.169 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.165, A:E.169, H2O.1 MG.6: 4 residues within 4Å: Chain A: T.17, D.90 Ligands: ADP.1, TYD.8 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.17, H2O.1, H2O.1, H2O.1 MG.10: 5 residues within 4Å: Chain B: Y.62, S.66, R.69, L.93, A.115 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.66 MG.11: 5 residues within 4Å: Chain B: E.39, P.40, F.65, D.68, R.69 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:F.65, B:D.68 MG.12: 3 residues within 4Å: Chain B: L.165, A.168, E.169 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:L.165, B:E.169

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

CL.7: 4 residues within 4Å: Chain A: E.169, P.170, G.171, R.172 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: P.124, R.172 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: G.3, L.4, F.5, R.125 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: G.13, S.14, G.15, K.16 Ligand excluded by PLIP

1 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.8: 14 residues within 4Å: Chain A: D.12, R.38, E.39, P.40, R.48, F.65, R.69, R.91, S.95, S.96, Y.99, Q.100, L.147 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.39, A:R.91, A:Y.99 Hydrogen bonds: A:R.38, A:R.69, A:R.69, A:Q.100, A:Q.100 Water bridges: A:T.17, A:D.90, A:R.91, A:R.91 Salt bridges: A:R.38, A:R.48, A:R.48, A:R.91 pi-Stacking: A:F.65

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

TMP.9: 12 residues within 4Å: Chain B: D.12, R.38, E.39, P.40, R.48, F.65, R.69, R.91, S.95, S.96, Y.99, Q.100 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:E.39, B:Y.99 Hydrogen bonds: B:R.69, B:Q.100, B:Q.100 Salt bridges: B:R.38, B:R.48 pi-Stacking: B:F.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaudhary, S.K. et al., Insights into product release dynamics through structural analyses of thymidylate kinase. Int. J. Biol. Macromol. (2018)

Release Date

2018-12-19

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate kinase

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