SMTL ID : 5mqj.1 (1 other biounit)

Crystal structure of dCK mutant C3S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

homo-dimer

Ligands

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 15 residues within 4Å: Chain A: N.50, A.52, A.53, G.54, K.55, S.56, T.57, R.209, L.212, R.213, D.262, F.263, K.264 Ligands: UMP.2, MG.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.57, A:F.263 Hydrogen bonds: A:A.52, A:A.53, A:G.54, A:K.55, A:S.56, A:T.57, A:T.57, A:T.57, A:D.262, A:F.263, A:K.264 Salt bridges: A:K.55, A:R.213, A:R.213 pi-Cation interactions: A:R.209 UDP.4: 16 residues within 4Å: Chain B: N.50, A.52, A.53, G.54, K.55, S.56, T.57, E.148, R.209, L.212, R.213, D.262, F.263, K.264 Ligands: UMP.5, MG.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:T.57, B:F.263 Hydrogen bonds: B:A.52, B:A.53, B:G.54, B:K.55, B:S.56, B:T.57, B:L.212, B:D.262, B:D.262, B:F.263, B:K.264 Salt bridges: B:K.55, B:R.213, B:R.213 pi-Cation interactions: B:R.209

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.2: 18 residues within 4Å: Chain A: I.51, A.52, K.55, E.74, W.79, L.103, M.106, Y.107, F.117, Q.118, R.149, D.154, F.158, R.213, R.215, E.218 Ligands: UDP.1, MG.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.51, A:W.79 Hydrogen bonds: A:A.52, A:E.74, A:Y.107, A:Y.107, A:Q.118, A:Q.118, A:E.218 Salt bridges: A:K.55, A:R.149, A:R.213, A:R.215 pi-Stacking: A:F.117 UMP.5: 21 residues within 4Å: Chain B: N.50, I.51, A.52, K.55, E.74, V.76, W.79, L.103, M.106, Y.107, F.117, Q.118, E.148, R.149, D.154, F.158, R.213, R.215, E.218 Ligands: UDP.4, MG.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.51, B:W.79, B:F.158 Hydrogen bonds: B:A.52, B:Y.107, B:Q.118, B:Q.118, B:E.218 Salt bridges: B:K.55, B:R.149, B:R.213, B:R.215 pi-Stacking: B:F.158

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: E.74, E.148, R.213 Ligands: UDP.1, UMP.2 No protein-ligand interaction detected (PLIP) MG.6: 7 residues within 4Å: Chain B: S.56, E.74, V.76, E.148, R.215 Ligands: UDP.4, UMP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.74, B:E.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hammam, K. et al., Dual protein kinase and nucleoside kinase modulators for rationally designed polypharmacology. Nat Commun (2017)

Release Date

2017-11-22

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Deoxycytidine kinase

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