SMTL ID : 3hp1.1

Crystal structure of human dCK R104M/D133A in complex with L-dT and ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 14 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, V.258, E.260, D.261, F.262 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:A.51, A:A.52, A:G.53, A:K.54, A:S.55, A:T.56, A:T.56, A:E.147, A:R.208, A:R.208, A:E.260, A:F.262 Water bridges: A:K.54, A:T.56, A:R.148, A:R.214, A:R.214, A:R.214, A:R.214 Salt bridges: A:K.54 pi-Cation interactions: A:R.208, A:R.208 ADP.3: 14 residues within 4Å: Chain B: A.51, A.52, G.53, K.54, S.55, T.56, E.147, R.208, L.211, R.212, V.258, E.260, D.261, F.262 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:A.51, B:A.52, B:G.53, B:K.54, B:S.55, B:T.56, B:T.56, B:E.147, B:R.208, B:E.260, B:F.262 Water bridges: B:K.54, B:T.56, B:R.148, B:R.214, B:R.214, B:R.214, B:R.214 Salt bridges: B:K.54 pi-Cation interactions: B:R.208, B:R.208

2 x LLT: L-deoxythymidine(Non-covalent)

LLT.2: 13 residues within 4Å: Chain A: E.73, V.75, W.78, L.102, M.105, Y.106, F.116, Q.117, M.124, R.148, A.153, F.157, E.217 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.78, A:L.102, A:F.116 Hydrogen bonds: A:E.73, A:Q.117, A:Q.117, A:R.148, A:E.217, A:E.217 pi-Stacking: A:F.157 LLT.4: 13 residues within 4Å: Chain B: E.73, V.75, W.78, L.102, M.105, Y.106, F.116, Q.117, M.124, R.148, A.153, F.157, E.217 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.78, B:L.102, B:F.116 Hydrogen bonds: B:E.73, B:Y.106, B:Q.117, B:Q.117, B:R.148, B:E.217 pi-Stacking: B:F.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hazra, S. et al., Extending Thymidine Kinase Activity to the Catalytic Repertoire of Human Deoxycytidine Kinase. Biochemistry (2009)

Release Date

2009-06-16

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Deoxycytidine kinase