SMTL ID : 5uiv.1

Structure of Thymidylate Kinase from Candida albicans Reveals Origin of Broad Substrate Specificity and a Novel Structural Element.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

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

TMP.1: 13 residues within 4Å: Chain A: K.38, F.39, P.40, R.42, L.54, F.70, R.74, R.95, S.99, G.100, Y.103, E.162, Y.164 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.39, A:Y.103 Hydrogen bonds: A:R.74, A:R.74 Water bridges: A:D.16, A:R.95, A:R.95, A:R.95, A:R.95, A:E.162, A:Y.164 Salt bridges: A:K.38, A:R.42, A:R.95 pi-Stacking: A:F.70 TMP.5: 13 residues within 4Å: Chain B: K.38, F.39, P.40, R.42, L.54, F.70, R.74, R.95, S.99, G.100, Y.103, E.162, Y.164 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.39, B:Y.103 Hydrogen bonds: B:R.74, B:R.74 Water bridges: B:D.16, B:R.95, B:R.95, B:R.95, B:R.95, B:Y.103, B:T.104, B:E.162 Salt bridges: B:K.38, B:R.42, B:R.95 pi-Stacking: B:F.70

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

ADP.2: 14 residues within 4Å: Chain A: L.15, D.16, R.17, S.18, G.19, K.20, S.21, T.22, R.156, K.157, K.197, T.198, I.199 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.17, A:S.18, A:G.19, A:K.20, A:S.21, A:S.21, A:T.22, A:T.22, A:R.156, A:R.156, A:K.157, A:K.197 Water bridges: A:K.20, A:K.20, A:K.20, A:K.157 Salt bridges: A:K.20 pi-Cation interactions: A:R.156, A:R.156 ADP.6: 14 residues within 4Å: Chain B: L.15, D.16, R.17, S.18, G.19, K.20, S.21, T.22, R.156, K.157, K.197, T.198, I.199 Ligands: MG.7 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.17, B:S.18, B:G.19, B:K.20, B:S.21, B:S.21, B:T.22, B:T.22, B:R.156, B:R.156, B:K.157, B:K.197 Water bridges: B:K.20, B:K.20, B:K.20, B:K.157 Salt bridges: B:K.20 pi-Cation interactions: B:R.156, B:R.156

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.16 Ligands: ADP.2, MG.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.16, H2O.1, H2O.2, H2O.3, H2O.3 MG.4: 5 residues within 4Å: Chain A: D.16, G.158, G.160, E.165 Ligands: MG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.16, A:G.158, A:E.165, H2O.2 MG.7: 3 residues within 4Å: Chain B: D.16 Ligands: ADP.6, MG.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.16, H2O.4, H2O.5, H2O.6, H2O.6 MG.8: 5 residues within 4Å: Chain B: D.16, G.158, G.160, E.165 Ligands: MG.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.16, B:D.16, B:G.158, B:E.165, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sinha, K. et al., The Structure of Thymidylate Kinase from Candida albicans Reveals a Unique Structural Element. Biochemistry (2017)

Release Date

2017-08-09

Peptides

Bifunctional thymidylate/uridylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Bifunctional thymidylate/uridylate kinase