SMTL ID : 2jat.1

Structure of deoxyadenosine kinase from M.mycoides with products dcmp and a flexible dcdp bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.14, D.77 Ligands: POP.2, DCM.3 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: DCM.3 MG.4: 4 residues within 4Å: Chain B: S.14, D.77 Ligands: POP.5, DCM.6 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: DCM.6

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 10 residues within 4Å: Chain A: T.8, G.10, A.11, G.12, K.13, S.14, T.15, R.145 Ligands: MG.1, DCM.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13, A:S.14, A:S.14, A:T.15, A:T.15 Salt bridges: A:K.13, A:R.145 POP.5: 10 residues within 4Å: Chain B: T.8, G.10, A.11, G.12, K.13, S.14, T.15, R.145 Ligands: MG.4, DCM.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.10, B:A.11, B:G.12, B:K.13, B:S.14, B:T.15 Salt bridges: B:K.13, B:R.145

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

DCM.3: 16 residues within 4Å: Chain A: T.8, V.9, K.13, V.33, F.39, Y.42, Y.43, M.53, Q.54, M.57, R.78, D.83, F.86, E.150 Ligands: MG.1, POP.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.9, A:F.86 Hydrogen bonds: A:Y.43, A:Q.54, A:D.83, A:D.83, A:E.150 Salt bridges: A:K.13, A:R.78 pi-Stacking: A:F.86 DCM.6: 14 residues within 4Å: Chain B: V.9, K.13, V.33, F.39, Y.42, Y.43, M.53, Q.54, R.78, D.83, F.86, E.150 Ligands: MG.4, POP.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.9, B:F.86 Hydrogen bonds: B:Y.42, B:Y.43, B:Y.43, B:Q.54, B:D.83, B:E.150 Salt bridges: B:K.13, B:R.78 pi-Stacking: B:F.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Welin, M. et al., Structure-Function Analysis of a Bacterial Deoxyadenosine Kinase Reveals the Basis for Substrate Specificity. J.Mol.Biol. (2007)

Release Date

2007-01-03

Peptides

DEOXYGUANOSINE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DEOXYGUANOSINE KINASE

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