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

Human Deoxycytidine kinase dCMP, UDP, Mg ion product complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: S.55, E.147, R.214 Ligands: UDP.2, DCM.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.55, A:E.147 MG.4: 5 residues within 4Å: Chain B: S.55, E.147, R.214 Ligands: UDP.5, DCM.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.55, B:E.147

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

UDP.2: 15 residues within 4Å: Chain A: A.51, A.52, G.53, K.54, S.55, T.56, E.147, R.208, L.211, R.212, E.260, D.261, F.262 Ligands: MG.1, DCM.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.262 Hydrogen bonds: A:A.51, A:G.53, A:K.54, A:S.55, A:S.55, A:T.56, A:T.56, A:T.56, A:E.147, A:D.261, A:F.262 Salt bridges: A:K.54, A:R.212, A:R.212 pi-Cation interactions: A:R.208 UDP.5: 15 residues within 4Å: Chain B: N.49, A.51, A.52, G.53, K.54, S.55, T.56, E.147, R.208, L.211, R.212, D.261, F.262 Ligands: MG.4, DCM.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.262 Hydrogen bonds: B:A.51, B:A.52, B:G.53, B:K.54, B:S.55, B:S.55, B:T.56, B:T.56, B:D.261, B:F.262 Salt bridges: B:K.54, B:R.212, B:R.212 pi-Cation interactions: B:R.208

2 x DCM: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DCM.3: 20 residues within 4Å: Chain A: I.50, A.51, K.54, E.73, W.78, L.102, M.105, Y.106, F.116, Q.117, R.124, E.147, R.148, D.153, F.157, R.212, R.214, E.217 Ligands: MG.1, UDP.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.50, A:W.78 Hydrogen bonds: A:A.51, A:Y.106, A:Y.106, A:Q.117, A:R.124, A:D.153, A:E.217 Salt bridges: A:K.54, A:R.148, A:R.212, A:R.214 pi-Stacking: A:F.157 DCM.6: 19 residues within 4Å: Chain B: I.50, A.51, K.54, E.73, W.78, L.102, Y.106, F.116, Q.117, R.124, E.147, R.148, D.153, F.157, R.212, R.214, E.217 Ligands: MG.4, UDP.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.78 Hydrogen bonds: B:A.51, B:Y.106, B:Q.117, B:R.124, B:D.153 Salt bridges: B:K.54, B:R.148, B:R.212, B:R.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Soriano, E.V. et al., Structures of human deoxycytidine kinase product complexes. Acta Crystallogr.,Sect.D (2007)

Release Date

2007-12-11

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Deoxycytidine kinase

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