SMTL ID : 5x8b.1

Crystal structure of ATP-TMP and ADP bound thymidylate kinase from Thermus thermophilus HB8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-dimer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain A: L.11, D.12, G.13, S.14, G.15, K.16, T.17, T.18, R.91, A.178, L.180, P.181, E.182, I.185 Ligands: TMP.2, MG.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:L.11, A:G.13, A:S.14, A:G.15, A:K.16, A:T.17, A:T.17, A:T.18, A:T.18, A:R.91, A:L.180 Water bridges: A:T.18 Salt bridges: A:K.16, A:K.16

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

TMP.2: 14 residues within 4Å: Chain A: D.12, E.39, P.40, R.48, F.65, R.69, R.91, S.95, S.96, Y.99, Q.100, L.147, L.150 Ligands: ATP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.39, A:F.65, A:R.91, A:Y.99 Hydrogen bonds: A:R.69, A:Q.100, A:Q.100 Water bridges: A:T.17 Salt bridges: A:R.48, A:R.91 pi-Stacking: A:F.65

7 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: T.17 Ligands: ATP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.17, H2O.1, H2O.2, H2O.3 MG.4: 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.5: 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 MG.6: 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.7: 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.8: 4 residues within 4Å: Chain B: L.11, D.12, Y.99, F.155 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.99, H2O.9 MG.9: 3 residues within 4Å: Chain B: T.17, D.90 Ligands: ADP.10 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.17, H2O.6, H2O.6, H2O.8, H2O.10

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

ADP.10: 16 residues within 4Å: Chain B: L.11, D.12, G.13, S.14, G.15, K.16, T.17, T.18, L.138, R.139, A.178, L.180, P.181, E.182, I.185 Ligands: MG.9 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:L.11, B:G.13, B:S.14, B:G.15, B:K.16, B:T.17, B:T.18, B:T.18, B:R.139, B:L.180 Water bridges: B:K.16, B:K.16, B:K.16, B:T.17, B:E.182 Salt bridges: B:K.16

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
A

B
B

Thymidylate kinase

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