SMTL ID : 5x86.1

Crystal structure of TMP bound thymidylate kinase from thermus thermophilus HB8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.19 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: G.13, S.14, G.15, K.16, T.17 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: G.13, S.14, G.15, K.16, T.17 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: Y.62, S.66, R.69, L.93, A.115 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.66 MG.3: 4 residues within 4Å: Chain A: Y.102, R.157, E.160, G.161 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:R.157, H2O.3, H2O.5, H2O.6 MG.4: 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.4 MG.5: 4 residues within 4Å: Chain A: E.160, L.163, A.164, R.167 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.160, A:E.160, H2O.6 MG.6: 4 residues within 4Å: Chain A: L.11, D.12, Y.99, F.155 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.99, H2O.1, H2O.3 MG.9: 5 residues within 4Å: Chain B: Y.62, S.66, R.69, L.93, A.115 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Y.62, B:S.66 MG.10: 3 residues within 4Å: Chain B: P.109, R.112, E.113 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:P.109, H2O.11 MG.11: 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.9

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

TMP.7: 11 residues within 4Å: Chain A: R.38, E.39, P.40, R.48, F.65, R.69, R.91, S.95, S.96, Y.99, Q.100 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.39, A:F.65, A:Y.99 Hydrogen bonds: A:R.69, A:Q.100, A:Q.100 Salt bridges: A:R.38, A:R.48 pi-Stacking: A:F.65 TMP.12: 14 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, L.147, L.150 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:E.39, B:F.65, B:R.91, B:Y.99 Hydrogen bonds: B:D.12, B:R.69, B:Q.100, B:Q.100 Water bridges: B:R.48, B:R.48 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., Structural and functional roles of dynamically correlated residues in thymidylate kinase. Acta Crystallogr D Struct Biol (2018)

Release Date

2018-03-14

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Thymidylate kinase

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