SMTL ID : 1ot3.2 (3 other biounits)

Crystal structure of Drosophila deoxyribonucleotide kinase complexed with the substrate deoxythymidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: N.28, I.29, G.30, S.31, G.32, K.33, T.34, R.167 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.30, A:S.31, A:G.32, A:K.33, A:T.34 Water bridges: A:K.33, A:R.105 Salt bridges: A:K.33, A:R.167 SO4.3: 8 residues within 4Å: Chain B: N.28, G.30, S.31, G.32, K.33, T.34, R.163, R.167 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.30, B:S.31, B:S.31, B:G.32, B:K.33, B:T.34, B:T.34 Water bridges: B:T.35, B:R.167 Salt bridges: B:K.33, B:R.167

2 x THM: THYMIDINE(Non-covalent)

THM.2: 15 residues within 4Å: Chain A: I.29, E.52, W.57, L.66, M.69, Y.70, F.80, Q.81, V.84, M.88, R.105, A.110, F.114, M.118, E.172 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.29, A:W.57, A:F.114 Hydrogen bonds: A:E.52, A:Y.70, A:Q.81, A:Q.81, A:R.105, A:E.172 Water bridges: A:R.105 pi-Stacking: A:F.114 THM.4: 13 residues within 4Å: Chain B: E.52, V.54, W.57, L.66, M.69, Y.70, F.80, Q.81, V.84, R.105, A.110, F.114, E.172 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.57, B:F.114, B:F.114 Hydrogen bonds: B:E.52, B:Q.81, B:Q.81, B:R.105, B:E.172, B:E.172 Water bridges: B:Y.179 pi-Stacking: B:F.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mikkelsen, N.E. et al., Structural Basis for Feedback Inhibition of the Deoxyribonucleoside Salvage Pathway: Studies of the Drosophila Deoxyribonucleoside Kinase. Biochemistry (2003)

Release Date

2003-05-27

Peptides

Deoxyribonucleoside Kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Deoxyribonucleoside Kinase

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