SMTL ID : 6ybh.1 (2 other biounits)

Deoxyribonucleoside Kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x 8LK: Pyrrolo-dC(Non-covalent)

8LK.1: 12 residues within 4Å: Chain A: I.18, E.41, W.46, Y.59, F.69, V.73, M.77, R.94, S.95, A.99, F.103, E.161 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.18, A:W.46, A:V.73, A:A.99 Hydrogen bonds: A:E.41, A:R.94, A:E.161 Water bridges: A:R.94 pi-Stacking: A:F.103, A:F.103 8LK.10: 11 residues within 4Å: Chain B: I.18, E.41, W.46, F.69, V.73, R.94, S.95, S.98, A.99, F.103, Y.168 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.18, B:W.46, B:V.73, B:A.99 Hydrogen bonds: B:E.41, B:R.94, B:Y.168 pi-Stacking: B:F.103, B:F.103

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

SO4.2: 3 residues within 4Å: Chain A: K.31, R.209, S.212 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.31, A:R.209 Salt bridges: A:R.209 SO4.3: 2 residues within 4Å: Chain A: R.152, N.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.199 Salt bridges: A:R.152 SO4.4: 5 residues within 4Å: Chain A: N.48, V.49, N.50, Y.72 Chain B: E.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.50, A:N.50 SO4.5: 8 residues within 4Å: Chain A: N.17, I.18, G.19, S.20, G.21, K.22, T.23, R.156 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.19, A:S.20, A:G.21, A:K.22, A:T.23, A:T.23 Water bridges: A:K.22, A:R.94 Salt bridges: A:K.22, A:R.156 SO4.6: 3 residues within 4Å: Chain A: T.85, N.86, K.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.86, A:K.87 Salt bridges: A:K.87 SO4.7: 7 residues within 4Å: Chain A: F.97, Y.101, W.179, P.186, Q.187, S.188, C.189 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.179, A:Q.187, A:S.188, A:S.188, A:C.189 SO4.11: 7 residues within 4Å: Chain B: N.17, I.18, G.19, S.20, G.21, K.22, T.23 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.19, B:S.20, B:G.21, B:K.22, B:T.23 Salt bridges: B:K.22 SO4.12: 3 residues within 4Å: Chain B: K.31, R.209, S.212 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.209 Salt bridges: B:K.31, B:R.209 SO4.13: 7 residues within 4Å: Chain B: I.96, F.97, R.100, Y.101, Y.125, I.128, E.129 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.100

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: K.2, E.5, H.133, I.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.2, A:I.134 GOL.9: 6 residues within 4Å: Chain A: S.71, L.121, W.124 Chain B: S.71, L.121, W.124 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.71 GOL.14: 3 residues within 4Å: Chain B: K.2, H.133, I.134 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.133, B:I.134 Water bridges: B:K.2, B:K.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Allouche-Arnon, H. et al., Computationally designed dual-color MRI reporters for noninvasive imaging of transgene expression. Nat.Biotechnol. (2022)

Release Date

2021-03-31

Peptides

Deoxynucleoside kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Deoxynucleoside kinase

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