SMTL ID : 2wwh.2 (1 other biounit)

Plasmodium falciparum thymidylate kinase in complex with AP5dT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x T5A: P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE(Non-covalent)

T5A.1: 28 residues within 4Å: Chain A: L.18, D.19, R.20, S.21, G.22, K.23, S.24, T.25, F.46, P.47, R.49, L.61, F.76, R.80, D.100, R.101, S.105, G.106, Y.109, R.147, S.148, Y.155, E.156, R.184, I.186, I.189 Ligands: NA.2, NA.3 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:F.46, A:F.76, A:Y.109 Hydrogen bonds: A:D.19, A:R.20, A:S.21, A:G.22, A:K.23, A:S.24, A:T.25, A:R.80, A:R.80, A:R.147, A:S.148, A:S.148, A:R.184 Water bridges: A:K.23, A:K.23, A:S.24, A:S.24, A:S.77, A:G.106, A:E.153 Salt bridges: A:R.20, A:K.23, A:K.23, A:K.23, A:R.49, A:R.101, A:R.101 pi-Stacking: A:F.76 pi-Cation interactions: A:R.147, A:R.147 T5A.4: 28 residues within 4Å: Chain B: L.18, D.19, R.20, S.21, G.22, K.23, S.24, T.25, F.46, P.47, R.49, L.61, F.76, R.80, D.100, R.101, S.105, G.106, Y.109, R.147, S.148, Y.155, E.156, R.184, I.186, I.189 Ligands: NA.5, NA.6 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:F.46, B:F.76, B:Y.109 Hydrogen bonds: B:D.19, B:D.19, B:R.20, B:S.21, B:G.22, B:K.23, B:S.24, B:T.25, B:T.25, B:R.80, B:R.80, B:S.148, B:S.148, B:E.156, B:R.184 Water bridges: B:K.23, B:K.23, B:S.24, B:S.24, B:S.77, B:G.106 Salt bridges: B:R.20, B:K.23, B:K.23, B:K.23, B:R.49, B:R.101, B:R.101 pi-Stacking: B:F.76 pi-Cation interactions: B:R.147, B:R.147

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: D.19, E.153, E.156 Ligands: T5A.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.19, A:R.20, A:E.153 NA.3: 3 residues within 4Å: Chain A: S.24, D.100 Ligands: T5A.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.24, A:D.100 Water bridges: A:S.24 NA.5: 4 residues within 4Å: Chain B: D.19, E.153, E.156 Ligands: T5A.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.19, B:R.20, B:E.153, B:E.156 NA.6: 3 residues within 4Å: Chain B: S.24, D.100 Ligands: T5A.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.24, B:D.100 Water bridges: B:S.24, B:D.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whittingham, J.L. et al., Structural Basis for the Efficient Phosphorylation of Aztmp and Dgmp by Plasmodium Falciparum Type I Thymidylate Kinase. Biochem.J. (2010)

Release Date

2010-04-21

Peptides

THYMIDILATE KINASE, PUTATIVE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

THYMIDILATE KINASE, PUTATIVE

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