SMTL ID : 5x7j.1

Crystal structure of thymidylate kinase from thermus thermophilus HB8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: E.169, P.170, G.171, R.172 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: K.123, P.124, R.172 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain A: G.13, S.14, G.15, K.16, T.17 Ligands: CA.5 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: L.4, F.5, R.125 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: K.123, P.124, R.172 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: E.169, P.170, G.171, R.172 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain B: Y.62, S.66, R.69, L.93, A.115, A.118 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: G.13, S.14, G.15, K.16, T.17 Ligands: CA.16 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: R.22, Q.190 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: A.136, R.140 Ligand excluded by PLIP

10 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: G.15, K.16, T.17, T.18 Ligands: CL.3 No protein-ligand interaction detected (PLIP) CA.6: 5 residues within 4Å: Chain A: G.10, L.11, L.130, D.131, L.132 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.130, H2O.2 CA.7: 6 residues within 4Å: Chain A: Y.62, S.66, R.69, L.93, A.115, A.118 No protein-ligand interaction detected (PLIP) CA.8: 5 residues within 4Å: Chain A: T.7, E.9, Y.92, D.94, T.127 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.7, A:E.9, A:D.94, H2O.3 CA.9: 4 residues within 4Å: Chain A: Q.19, R.22, L.23, I.189 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Q.19, H2O.2 CA.16: 4 residues within 4Å: Chain B: G.15, T.17, T.18 Ligands: CL.13 No protein-ligand interaction detected (PLIP) CA.17: 4 residues within 4Å: Chain B: D.12, Y.99, R.143, F.155 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Y.99 CA.18: 5 residues within 4Å: Chain B: T.7, E.9, Y.92, D.94, T.127 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.7, B:E.9, B:D.94, H2O.7 CA.19: 5 residues within 4Å: Chain B: Q.19, R.22, L.23, A.186, Q.190 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Q.19 CA.20: 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

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

EDO.21: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.21, B:E.182 EDO.22: 4 residues within 4Å: Chain B: A.166, R.167, P.170, V.175 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.167, B:P.170, B:F.173 EDO.23: 5 residues within 4Å: Chain B: L.126, P.170, G.171, F.173, V.174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.173 Water bridges: B:V.175 EDO.24: 2 residues within 4Å: Chain B: R.32, P.198 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.32, B:R.32

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. (2019)

Release Date

2018-03-07

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate kinase

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