SMTL ID : 7v1i.1

Crystal structure of Omsk hemorrhagic fever virus NS5 MTase (with an m7GMP-Arg28 adduct and in complex with SAH)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: R.32, R.36, R.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.32, A:R.36, A:R.36

1 x G7M: N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE(Covalent)

G7M.2: 13 residues within 4Å: Chain A: K.8, L.11, N.12, C.14, F.19, R.23, S.145, S.146, P.147, R.209, S.211 Ligands: MGP.3, MG.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.8, A:K.8, A:L.11, A:S.145 Water bridges: A:C.14, A:T.15, A:S.145, A:S.145, A:R.209 Salt bridges: A:R.23, A:R.209 pi-Stacking: A:F.19, A:F.19

1 x MGP: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE(Covalent)

MGP.3: 13 residues within 4Å: Chain A: K.8, L.11, N.12, C.14, F.19, R.23, S.145, S.146, P.147, R.209, S.211 Ligands: G7M.2, MG.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.8, A:K.8, A:L.11, A:S.145, A:S.145, A:S.145, A:S.211 Water bridges: A:C.14, A:T.15, A:R.209, A:R.209 Salt bridges: A:R.23, A:R.23, A:R.209, A:R.209 pi-Stacking: A:F.19, A:F.19

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4: 17 residues within 4Å: Chain A: S.51, G.53, G.76, C.77, G.78, G.80, G.81, W.82, T.99, I.100, H.105, M.125, D.126, V.127, F.128, D.141, I.142 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.51, A:G.80, A:G.81, A:W.82, A:W.82, A:W.82, A:T.99, A:I.100, A:E.106, A:D.126, A:D.126, A:V.127, A:D.141 Water bridges: A:R.79, A:G.143

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.5: 2 residues within 4Å: Ligands: G7M.2, MGP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jia, H. et al., Crystal Structures of Flavivirus NS5 Guanylyltransferase Reveal a GMP-Arginine Adduct. J.Virol. (2022)

Release Date

2022-06-15

Peptides

Core protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Core protein

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