SMTL ID : 5xt8.1

Magnesium bound apo structure of thymidylate kinase (form I) from Thermus thermophilus HB8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: L.176, H.192 No protein-ligand interaction detected (PLIP) MG.2: 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.3: 5 residues within 4Å: Chain A: T.7, E.9, Y.92, D.94, T.127 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.7, A:E.9, A:D.94 MG.4: 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.1 MG.5: 4 residues within 4Å: Chain A: G.15, T.17, T.18 Ligands: CL.9 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: A.83 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.83 MG.13: 4 residues within 4Å: Chain B: K.123, E.169, R.172 Ligands: CL.17 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.169 MG.14: 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.8 MG.15: 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.16: 4 residues within 4Å: Chain B: L.129, D.131, R.159, Y.162 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.131

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

CL.6: 2 residues within 4Å: Chain A: A.136, R.139 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: K.123, P.124, R.172 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: E.169, P.170, G.171, R.172 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain A: G.13, S.14, G.15, K.16, T.17 Ligands: MG.5 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain B: E.169, P.170, G.171, R.172 Ligands: MG.13 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain B: L.11, G.13, S.14, G.15, K.16, T.17 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: K.123, P.124, R.172 Ligand excluded by PLIP

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

EDO.10: 6 residues within 4Å: Chain A: R.140, A.178, L.180, P.181, E.182, I.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.140 EDO.11: 3 residues within 4Å: Chain A: F.173, V.174, V.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.175 EDO.20: 2 residues within 4Å: Chain B: P.133, R.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.159, B:R.159

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

2018-04-18

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate kinase

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