SMTL ID : 5x6z.1 (1 other biounit)

Crystal structure of Rice Dwarf Virus P5 in complex with GTP and GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

GTP.1: 17 residues within 4Å: Chain A: Q.619, P.625, K.630, Y.648, R.651, I.704, S.705, G.706, H.707, W.725, M.729, D.749, N.750, K.751, W.761, H.762 Ligands: GDP.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:Q.619, A:Q.619, A:Q.619, A:I.704, A:G.706, A:H.707, A:N.750, A:K.751, A:K.751 Water bridges: A:S.710 Salt bridges: A:K.630, A:K.630, A:R.651, A:H.707, A:H.707, A:H.762 pi-Stacking: A:W.761, A:W.761, A:W.761 GTP.3: 15 residues within 4Å: Chain B: Q.619, K.630, Y.648, R.651, N.703, I.704, G.706, H.707, W.725, M.729, N.750, K.751, W.761, H.762 Ligands: GDP.2 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:Y.648, B:Y.648, B:Y.648, B:N.703, B:G.706, B:W.725, B:N.750, B:N.750, B:K.751, B:K.751 Water bridges: B:Q.619, B:K.630, B:H.707, B:H.707, B:H.707 Salt bridges: B:K.630, B:K.630, B:R.651, B:H.707, B:H.762 pi-Stacking: B:W.761, B:W.761, B:W.761 pi-Cation interactions: B:W.761, B:W.761

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 11 residues within 4Å: Chain A: D.53, M.56, S.57, E.137, V.140 Chain B: Y.76, R.80, K.630, H.644, K.751 Ligands: GTP.3 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.76, B:Y.76 Water bridges: B:E.645 Salt bridges: B:R.80, B:R.80, B:K.630, B:K.751, A:D.53, A:E.137 GDP.4: 11 residues within 4Å: Chain A: Y.76, R.80, H.644, Y.648 Chain B: Y.50, D.53, M.56, S.57, E.137, V.140 Ligands: GTP.1 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.76, A:Y.648, A:Y.648 Water bridges: A:H.644, B:K.49 Salt bridges: A:R.80, A:K.630, B:D.53, B:E.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamichi, Y. et al., Crystal structure of the capping enzyme P5 from Rice Dwarf Virus. To Be Published

Release Date

2018-02-28

Peptides

mRNA capping enzyme P5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

mRNA capping enzyme P5

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