SMTL ID : 6kwq.1

Crystal structure of enterovirus 71 polymerase elongation complex (native form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: D.233, D.330, T.373 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.330, H2O.3, H2O.3, H2O.7, H2O.8, H2O.11 MG.2: 2 residues within 4Å: Chain A: N.106, H.199 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain B: G.27 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain B: A.18 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain B: G.2 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: 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

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 7 residues within 4Å: Chain A: I.3, V.6, E.55, F.59, Y.276, K.279, Y.281 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.55 Water bridges: A:K.279

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: K.159, R.174 Chain B: G.20 Chain C: A.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.174 Water bridges: A:R.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, W. et al., A nucleobase-binding pocket in a viral RNA-dependent RNA polymerase contributes to elongation complex stability. Nucleic Acids Res. (2020)

Release Date

2019-12-11

Peptides

RNA-dependent RNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-dependent RNA polymerase

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