SMTL ID : 2zxu.3 (2 other biounits)

Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe) and DMASPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

2 x DST: DIMETHYLALLYL S-THIOLODIPHOSPHATE(Non-covalent)

DST.1: 15 residues within 4Å: Chain A: P.18, T.19, A.20, S.21, G.22, K.23, T.24, G.53, T.54, A.55, R.217, M.221, L.278 Chain C: A.37 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.55, A:L.278 Hydrogen bonds: A:A.20, A:S.21, A:G.22, A:K.23, A:K.23, A:K.23, A:T.24, A:R.217 Water bridges: A:G.22, A:T.24, A:R.217 Salt bridges: A:K.23, A:R.217 DST.3: 15 residues within 4Å: Chain B: T.19, A.20, S.21, G.22, K.23, T.24, G.53, T.54, A.55, R.217, V.249, T.275, L.278 Chain D: A.37 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.19, B:A.55, B:L.278 Hydrogen bonds: B:A.20, B:S.21, B:G.22, B:K.23, B:K.23, B:K.23, B:T.24, B:R.217 Salt bridges: B:K.23, B:R.217

10 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 3 residues within 4Å: Chain A: T.24, A.55 Ligands: DST.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.24 MG.4: 3 residues within 4Å: Chain B: T.24, A.55 Ligands: DST.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.24 MG.5: 3 residues within 4Å: Chain C: U.16, C.17, G.19 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain C: G.27 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain C: A.7, U.8, A.14 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain C: U.51, U.59, U.60 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain C: A.58, U.59 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain C: G.22, U.45, G.46 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain C: U.8, U.12 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain D: G.27 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chimnaronk, S. et al., Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon. Biochemistry (2009)

Release Date

2009-05-26

Peptides

tRNA delta(2)-isopentenylpyrophosphate transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

tRNA delta(2)-isopentenylpyrophosphate transferase

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