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

Structure of the NS5 methyltransferase from Zika bound to MS2042

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x KB1: 5'-{[(3S)-3-amino-3-carboxypropyl][(4-fluorophenyl)methyl]amino}-5'-deoxyadenosine(Non-covalent)

KB1.1: 22 residues within 4Å: Chain A: S.56, G.58, G.81, C.82, G.83, G.85, G.86, W.87, T.104, K.105, H.110, V.130, D.131, V.132, F.133, D.146, I.147, G.148, E.149, K.182 Ligands: CL.4, IPA.8 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.56, A:G.85, A:G.86, A:W.87, A:W.87, A:W.87, A:T.104, A:K.105, A:H.110, A:D.131, A:V.132 Water bridges: A:R.84, A:S.88, A:E.111, A:E.111, A:Y.220 Salt bridges: A:D.146 pi-Cation interactions: A:K.105

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: G.148, E.149, R.160 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: A.225, K.226 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: I.147, G.148, E.149 Ligands: KB1.1 Ligand excluded by PLIP

3 x URE: UREA(Non-functional Binders)

URE.5: 5 residues within 4Å: Chain A: R.37, R.41, V.55, R.57, R.84 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.37, A:R.41, A:V.55, A:R.57, A:R.57 Water bridges: A:R.84 URE.6: 5 residues within 4Å: Chain A: L.71, Q.72, A.178, S.223, G.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.72, A:Q.72, A:G.177 URE.7: 3 residues within 4Å: Chain A: L.162, L.165, S.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.162

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.8: 5 residues within 4Å: Chain A: S.56, R.57, G.58, K.61 Ligands: KB1.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.61, A:K.61

1 x NA: SODIUM ION(Non-functional Binders)

NA.9: 3 residues within 4Å: Chain A: G.107, H.110, E.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.110, A:H.110, A:E.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jain, R. et al., Development of a S-adenosylmethionine analog that intrudes the RNA-cap binding site of Zika methyltransferase. Sci Rep (2017)

Release Date

2017-05-17

Peptides

MRNA cap 0-1 NS5-type methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

MRNA cap 0-1 NS5-type methyltransferase

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