SMTL ID : 2p3q.2 (1 other biounit)

Crystal Structure of Dengue Methyltransferase in Complex with GpppG and S-Adenosyl-L-homocysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: R.47, K.51, V.64, S.65, R.66, R.93 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.66 Salt bridges: A:R.47, A:K.51, A:R.66, A:R.93 SO4.2: 3 residues within 4Å: Chain A: E.58, H.61, H.62 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.62 SO4.3: 3 residues within 4Å: Chain A: H.61, G.268, S.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.269 Salt bridges: A:H.61 SO4.4: 6 residues within 4Å: Chain A: K.114, D.140, R.172 Chain B: V.165, R.169 Ligands: SAH.8 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.140 Salt bridges: A:K.114, A:R.172, B:R.169 SO4.5: 7 residues within 4Å: Chain A: S.159, S.160, P.161, V.165, R.169 Chain B: K.114, H.119 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.114, B:H.119, A:R.169 Hydrogen bonds: A:E.158 SO4.6: 4 residues within 4Å: Chain A: G.118, H.119, E.120 Ligands: SAH.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.120 Salt bridges: A:H.119 SO4.9: 6 residues within 4Å: Chain B: R.47, K.51, V.64, S.65, R.66, R.93 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.66 Salt bridges: B:R.47, B:K.51, B:R.66, B:R.93 SO4.10: 3 residues within 4Å: Chain B: E.58, H.61, H.62 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.62 SO4.11: 3 residues within 4Å: Chain B: H.61, G.268, S.269 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.269 Salt bridges: B:H.61 SO4.12: 6 residues within 4Å: Chain A: V.165, R.169 Chain B: K.114, D.140, R.172 Ligands: SAH.16 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.114, B:R.172, A:R.169 SO4.13: 7 residues within 4Å: Chain A: K.114, H.119 Chain B: S.159, S.160, P.161, V.165, R.169 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.114, A:H.119, B:R.169 SO4.14: 4 residues within 4Å: Chain B: G.118, H.119, E.120 Ligands: SAH.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.120 Salt bridges: B:H.119

2 x GP3: DIGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GP3.7: 11 residues within 4Å: Chain A: K.23, L.26, N.27, L.29, F.34, K.38, S.159, S.160, P.161, E.166, S.223 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.23, A:N.27, A:L.29, A:L.29, A:L.29, A:S.159, A:S.160 Salt bridges: A:K.38 pi-Stacking: A:F.34, A:F.34 GP3.15: 11 residues within 4Å: Chain B: K.23, L.26, N.27, L.29, F.34, K.38, S.159, S.160, P.161, E.166, S.223 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.23, B:N.27, B:L.29, B:L.29, B:L.29, B:S.159, B:S.160, B:E.166 Salt bridges: B:K.38 pi-Stacking: B:F.34, B:F.34

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

SAH.8: 18 residues within 4Å: Chain A: S.65, G.67, G.90, C.91, G.92, G.94, G.95, W.96, T.113, K.114, V.139, D.140, V.141, F.142, D.155, I.156 Ligands: SO4.4, SO4.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.65, A:G.67, A:C.91, A:G.94, A:G.95, A:W.96, A:W.96, A:K.114, A:D.140, A:V.141 pi-Cation interactions: A:K.114 SAH.16: 18 residues within 4Å: Chain B: S.65, G.67, G.90, C.91, G.92, G.94, G.95, W.96, T.113, K.114, V.139, D.140, V.141, F.142, D.155, I.156 Ligands: SO4.12, SO4.14 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.65, B:G.67, B:C.91, B:G.94, B:G.95, B:W.96, B:W.96, B:T.113, B:K.114, B:D.140, B:V.141, B:D.155 pi-Cation interactions: B:K.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egloff, M.P. et al., Structural and functional analysis of methylation and 5'-RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5. J.Mol.Biol. (2007)

Release Date

2007-08-28

Peptides

type II methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

type II methyltransferase

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