SMTL ID : 3ffu.1

Structure of the RNA pyrophosphohydrolase BdRppH in complex with GTP and magnesium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 18 residues within 4Å: Chain A: V.24, R.40, N.44, L.46, E.51, F.52, G.54, G.55, K.56, E.70, E.74, Y.92, I.97, P.133, N.136 Ligands: MG.2, MG.3, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.44, A:F.52, A:F.52, A:F.52, A:K.56, A:N.136 Water bridges: A:G.54, A:G.54, A:E.73 Salt bridges: A:R.40, A:E.51, A:K.56, A:K.56, A:K.56 GTP.5: 19 residues within 4Å: Chain B: V.24, R.40, N.44, L.46, E.51, F.52, G.54, G.55, K.56, E.70, E.74, Y.92, I.97, I.99, P.133, N.136 Ligands: MG.6, MG.7, MG.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:F.52, B:F.52, B:F.52, B:K.56, B:E.70, B:N.136 Water bridges: B:G.54, B:G.54, B:R.69, B:E.74, B:E.74 Salt bridges: B:R.40, B:E.51, B:K.56, B:K.56, B:K.56

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: R.69, E.70, E.73 Ligands: GTP.1, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.70, A:E.70, H2O.1, H2O.1, H2O.1 MG.3: 7 residues within 4Å: Chain A: G.54, E.70, E.73, E.74 Ligands: GTP.1, MG.2, MG.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.70, A:E.74, H2O.1, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain A: G.54, E.74 Ligands: GTP.1, MG.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.54, A:E.74, A:E.74, H2O.1, H2O.1 MG.6: 6 residues within 4Å: Chain B: E.58, R.69, E.70, E.73 Ligands: GTP.5, MG.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.70, H2O.1, H2O.1, H2O.1 MG.7: 6 residues within 4Å: Chain B: E.70, E.73, E.74 Ligands: GTP.5, MG.6, MG.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.70, B:E.74, H2O.1, H2O.1, H2O.1 MG.8: 5 residues within 4Å: Chain B: G.54, E.70, E.74 Ligands: GTP.5, MG.7 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:G.54, B:E.74, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Messing, S.A. et al., Structure and Biological Function of the RNA Pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus. Structure (2009)

Release Date

2009-03-24

Peptides

Probable pyrophosphohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable pyrophosphohydrolase

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