SMTL ID : 2jj8.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: N.28, I.29, G.30, K.33, E.52, R.105 Ligands: SO4.2, AZZ.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.30, A:E.52 Salt bridges: A:K.33, A:R.105 SO4.2: 8 residues within 4Å: Chain A: N.28, I.29, G.30, S.31, G.32, K.33, T.34 Ligands: SO4.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.30, A:S.31, A:G.32, A:K.33, A:T.34 Salt bridges: A:K.33 SO4.4: 8 residues within 4Å: Chain B: N.28, I.29, G.30, S.31, G.32, K.33, T.34 Ligands: SO4.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.30, B:S.31, B:G.32, B:K.33, B:T.34, B:E.104 Salt bridges: B:K.33 SO4.5: 7 residues within 4Å: Chain B: N.28, I.29, K.33, E.52, R.105 Ligands: SO4.4, AZZ.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.30, B:E.52 Salt bridges: B:K.33, B:R.105

2 x AZZ: 3'-azido-3'-deoxythymidine(Non-covalent)

AZZ.3: 11 residues within 4Å: Chain A: E.52, V.54, W.57, F.80, Q.81, V.84, M.88, R.105, A.110, F.114 Ligands: SO4.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.57, A:F.114, A:F.114 Hydrogen bonds: A:E.52, A:Q.81, A:Q.81, A:R.105 pi-Stacking: A:F.114 AZZ.6: 13 residues within 4Å: Chain B: E.52, W.57, L.66, Y.70, F.80, Q.81, V.84, M.88, R.105, A.110, F.114, M.118 Ligands: SO4.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.57, B:V.84, B:F.114, B:F.114 Hydrogen bonds: B:E.52, B:Y.70, B:Q.81, B:Q.81, B:R.105 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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