SMTL ID : 3gru.1

Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 11 residues within 4Å: Chain A: Q.30, I.78, E.79, I.80, D.81, G.103, D.104, A.105, P.123, Y.124, I.126 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:I.80, A:D.104, A:D.104, A:A.105, A:Y.124 Water bridges: A:L.59, A:L.59, A:D.81, A:D.81

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

SO4.2: 2 residues within 4Å: Chain A: K.152 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.148, A:K.152 Salt bridges: A:K.152 SO4.3: 3 residues within 4Å: Chain A: Y.148, K.181 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.148 Water bridges: A:K.181 Salt bridges: A:K.152, A:K.181 SO4.4: 1 residues within 4Å: Chain A: K.232 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.228, A:K.228 Salt bridges: A:K.232 SO4.5: 1 residues within 4Å: Chain A: R.165 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

O'Farrell, H.C. et al., Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design. Biochemistry (2010)

Release Date

2010-03-31

Peptides

Dimethyladenosine transferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dimethyladenosine transferase

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