SMTL ID : 2vp0.1

Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.34, E.52, E.104 Ligands: TTP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.34, A:E.52, A:E.104, H2O.1 MG.3: 5 residues within 4Å: Chain B: T.34, E.52, E.104, R.169 Ligands: TTP.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.34, B:E.52, B:E.104

2 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.2: 25 residues within 4Å: Chain A: N.28, I.29, G.30, S.31, G.32, K.33, T.34, E.52, V.54, W.57, L.66, M.69, Y.70, F.80, Q.81, V.84, E.104, R.105, A.110, F.114, M.118, R.167, R.169, E.172 Ligands: MG.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:I.29, A:W.57, A:W.57, A:F.114, A:F.114 Hydrogen bonds: A:G.30, A:S.31, A:G.32, A:K.33, A:T.34, A:Q.81, A:Q.81, A:E.172, A:E.172 Water bridges: A:T.34, A:E.52, A:E.52, A:R.169 Salt bridges: A:K.33, A:K.33, A:K.33, A:R.105, A:R.167, A:R.167, A:R.169 pi-Stacking: A:F.114 TTP.4: 25 residues within 4Å: Chain B: N.28, I.29, G.30, S.31, G.32, K.33, T.34, E.52, V.54, W.57, L.66, M.69, Y.70, F.80, Q.81, V.84, E.104, R.105, A.110, F.114, M.118, R.167, R.169, E.172 Ligands: MG.3 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.29, B:W.57, B:W.57, B:F.114, B:F.114 Hydrogen bonds: B:N.28, B:G.30, B:S.31, B:G.32, B:K.33, B:T.34, B:Q.81, B:Q.81, B:E.172, B:E.172 Water bridges: B:T.35 Salt bridges: B:K.33, B:K.33, B:K.33, B:R.105, B:R.167, B:R.167, B:R.169 pi-Stacking: B:F.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mikkelsen, N.E. et al., Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase. FEBS J. (2008)

Release Date

2008-04-29

Peptides

DEOXYNUCLEOSIDE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DEOXYNUCLEOSIDE KINASE

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