SMTL ID : 7w9s.1

Crystal structure of the enterovirus 71 polymerase elongation complex (C1S3 form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

monomer

Ligands

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.1: 17 residues within 4Å: Chain A: K.167, R.174, D.233, Y.234, S.235, G.236, Y.237, D.238, S.289, T.294, N.298, D.329, K.360 Chain B: G.20 Chain C: A.16 Ligands: MG.6, MG.7 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.174, A:Y.234, A:G.236, A:Y.237, A:D.238, A:D.238, A:S.289, A:S.289, A:N.298 Water bridges: A:R.163, A:K.167, A:K.167 Salt bridges: A:K.167, A:R.174, A:R.174, A:K.360, A:K.360

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

SO4.2: 4 residues within 4Å: Chain A: K.38, R.163, S.164, K.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.164 Salt bridges: A:K.38, A:R.163, A:K.167 SO4.3: 5 residues within 4Å: Chain A: W.5, T.12, R.14, H.273, T.280 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.14, A:H.273 SO4.4: 5 residues within 4Å: Chain A: C.212, N.213, T.216, F.217, K.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.213, A:T.216, A:T.216, A:F.217 Salt bridges: A:K.220

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: W.5, H.271, H.273, C.282 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.271, A:H.273, A:C.282

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 6 residues within 4Å: Chain A: D.233, D.329, D.330 Chain C: A.16 Ligands: CTP.1, MG.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.233, A:D.329, A:D.330 MG.7: 5 residues within 4Å: Chain A: D.233, Y.234, D.329 Ligands: CTP.1, MG.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.233, A:Y.234, A:D.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, R. et al., Crystal structure of a pre-chemistry viral RNA-dependent RNA polymerase suggests participation of two basic residues in catalysis. Nucleic Acids Res. (2022)

Release Date

2022-11-16

Peptides

Genome polyprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Genome polyprotein

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