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

Plasmodium falciparum thymidylate kinase in complex with TMP and ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

TMP.1: 13 residues within 4Å: Chain A: D.19, F.46, P.47, R.49, L.61, F.76, R.80, R.101, S.105, G.106, Y.109, Y.155 Ligands: NA.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.46, A:R.101, A:Y.109 Hydrogen bonds: A:D.19, A:R.80, A:R.80 Water bridges: A:K.23, A:K.23, A:K.23, A:R.49, A:S.77, A:R.101, A:G.106, A:S.110, A:Y.155 Salt bridges: A:K.23, A:R.49, A:R.101 pi-Stacking: A:F.76 TMP.9: 13 residues within 4Å: Chain B: D.19, F.46, P.47, R.49, L.61, F.76, R.80, R.101, S.105, G.106, Y.109, Y.155 Ligands: NA.11 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.46, B:R.101, B:Y.109 Hydrogen bonds: B:D.19, B:D.19, B:R.80, B:R.80 Water bridges: B:K.23, B:K.23, B:K.23, B:R.49, B:S.77, B:R.101, B:G.106, B:S.110, B:E.153 Salt bridges: B:K.23, B:R.49, B:R.101 pi-Stacking: B:F.76

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

ADP.2: 12 residues within 4Å: Chain A: R.20, S.21, G.22, K.23, S.24, T.25, R.147, S.148, R.184, I.186, I.189 Ligands: NA.4 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:R.20, A:S.21, A:G.22, A:K.23, A:S.24, A:T.25, A:T.25, A:R.147, A:S.148, A:R.184 Water bridges: A:K.23, A:K.23, A:K.23, A:S.24, A:S.24, A:S.24, A:S.24, A:T.25, A:R.147, A:R.147, A:S.148, A:S.148, A:I.186 Salt bridges: A:K.23 pi-Cation interactions: A:R.147, A:R.147 ADP.10: 12 residues within 4Å: Chain B: R.20, S.21, G.22, K.23, S.24, T.25, R.147, S.148, R.184, I.186, I.189 Ligands: NA.12 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:R.20, B:S.21, B:G.22, B:K.23, B:S.24, B:T.25, B:T.25, B:R.147, B:S.148, B:R.184 Water bridges: B:K.23, B:K.23, B:K.23, B:S.24, B:S.24, B:S.24, B:S.24, B:T.25, B:R.147, B:R.147, B:S.148, B:S.148, B:I.186 Salt bridges: B:K.23 pi-Cation interactions: B:R.147, B:R.147

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

NA.3: 3 residues within 4Å: Chain A: D.19, E.156 Ligands: TMP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.156 Water bridges: A:R.20 NA.4: 2 residues within 4Å: Chain A: S.24 Ligands: ADP.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.24 Water bridges: A:K.23, A:S.24, A:S.24, A:D.100, A:D.100 NA.8: 1 residues within 4Å: Chain A: W.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.174 Water bridges: A:N.179 NA.11: 3 residues within 4Å: Chain B: D.19, E.156 Ligands: TMP.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.19, B:E.156, B:E.156 Water bridges: B:R.20 NA.12: 2 residues within 4Å: Chain B: S.24 Ligands: ADP.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.24, B:S.24 Water bridges: B:K.23, B:S.24 NA.16: 1 residues within 4Å: Chain B: W.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.177 Water bridges: B:N.179

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 1 residues within 4Å: Chain A: E.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.40 GOL.6: 7 residues within 4Å: Chain A: E.70, L.116, N.117, W.120 Chain B: W.81, Q.126, G.127 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.70, A:E.70, A:N.117, B:Q.126 Water bridges: A:N.117 GOL.7: 5 residues within 4Å: Chain A: N.48, T.51, E.82, H.83, E.86 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.48, A:E.86, A:E.86 Water bridges: A:N.48, A:E.86 GOL.13: 1 residues within 4Å: Chain B: E.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.40 Water bridges: B:E.40 GOL.14: 7 residues within 4Å: Chain A: W.81, Q.126, G.127 Chain B: E.70, L.116, N.117, W.120 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.70, B:N.117, A:Q.126 Water bridges: B:N.117 GOL.15: 5 residues within 4Å: Chain B: N.48, T.51, E.82, H.83, E.86 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.48, B:E.86 Water bridges: B:N.48, B:E.86

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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