SMTL ID : 3eph.1 (2 other biounits)

Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.363, C.366, H.385, H.391 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.363, A:C.366, A:H.385, A:H.391 ZN.9: 4 residues within 4Å: Chain C: C.363, C.366, H.385, H.391 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.363, C:C.366, C:H.385, C:H.391

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

MG.2: 3 residues within 4Å: Chain A: S.16, Q.37 Ligands: PPV.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.16 MG.3: 3 residues within 4Å: Chain A: K.282, K.286 Chain B: C.26 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: Q.17 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: W.67 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain B: G.11 No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain C: S.16 Ligands: PPV.13 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.16, H2O.202, H2O.225 MG.11: 1 residues within 4Å: Chain C: Q.17 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain C: D.66 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain D: G.51 No protein-ligand interaction detected (PLIP)

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.6: 10 residues within 4Å: Chain A: T.11, G.12, V.13, G.14, K.15, S.16, Q.37, N.47, R.208 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.12, A:V.13, A:G.14, A:K.15, A:S.16, A:Q.37, A:N.47, A:R.208 Water bridges: A:K.15, A:K.15, A:K.15, A:Q.17, A:Q.17, A:G.99 Salt bridges: A:K.15, A:K.15, A:R.208 PPV.13: 11 residues within 4Å: Chain C: T.10, T.11, G.12, V.13, G.14, K.15, S.16, Q.37, N.47, R.208 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.12, C:V.13, C:G.14, C:K.15, C:S.16, C:Q.37, C:N.47 Water bridges: C:K.15, C:K.15, C:K.15, C:S.16 Salt bridges: C:K.15, C:K.15, C:R.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, C. et al., Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-11-04

Peptides

tRNA isopentenyltransferase: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

tRNA isopentenyltransferase

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