SMTL ID : 4hdg.3 (2 other biounits)

Crystal Structure of viral RdRp in complex with GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

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

GTP.1: 16 residues within 4Å: Chain A: R.194, K.197, K.205, R.208, D.275, G.337, S.338, N.347, D.402, D.403, S.449, R.468, R.476, S.533, W.534, S.535 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:R.194, A:K.205, A:R.208, A:S.338, A:N.347, A:S.449, A:S.533, A:W.534, A:S.535 Water bridges: A:D.275, A:D.402, A:D.402, A:S.535 Salt bridges: A:K.197, A:K.197, A:K.197, A:R.208, A:D.275, A:D.402, A:R.468, A:R.476, A:R.476 pi-Cation interactions: A:R.208 GTP.4: 14 residues within 4Å: Chain B: R.194, K.197, K.205, R.208, D.275, S.338, N.347, D.402, D.403, R.468, R.476, S.533, W.534, S.535 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:K.205, B:R.208, B:S.338, B:N.347, B:S.449, B:S.533, B:W.534, B:S.535 Water bridges: B:S.535, B:S.535 Salt bridges: B:R.194, B:K.197, B:K.197, B:K.197, B:R.208, B:D.275, B:D.402, B:R.468, B:R.476, B:R.476 pi-Cation interactions: B:R.208

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: E.174, H.178, C.183, H.184, C.186 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.174, A:H.178, A:C.183, A:C.186 ZN.3: 3 residues within 4Å: Chain A: H.451, C.467, C.586 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.451, A:C.467, A:C.586, H2O.9 ZN.5: 5 residues within 4Å: Chain B: E.174, H.178, C.183, H.184, C.186 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.174, B:H.178, B:C.183, B:C.186 ZN.6: 3 residues within 4Å: Chain B: H.451, C.467, C.586 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.451, B:C.467, B:C.586, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Surana, P. et al., RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state. Nucleic Acids Res. (2014)

Release Date

2013-12-25

Peptides

Polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Polyprotein

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