SMTL ID : 4dcd.1

1.6A resolution structure of PolioVirus 3C Protease Containing a covalently bound dipeptidyl inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.1: 3 residues within 4Å: Chain A: H.5, H.6, H.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.6

1 x K36: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

K36.2: 16 residues within 4Å: Chain A: H.47, E.78, N.133, L.134, G.135, R.137, T.149, R.150, A.151, C.154, H.168, V.169, G.170, G.171, N.172, F.177 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.47, A:L.134, A:L.134, A:R.137, A:N.172, A:F.177 Hydrogen bonds: A:L.134, A:T.149, A:V.169, A:G.171 Water bridges: A:R.150, A:C.154

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

SO4.3: 4 residues within 4Å: Chain A: H.4, H.5, G.8, P.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.5, A:H.7 Salt bridges: A:H.4, A:H.5 SO4.4: 3 residues within 4Å: Chain A: R.86, N.87, E.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.87, A:E.88 Water bridges: A:R.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Broad-Spectrum Antivirals against 3C or 3C-Like Proteases of Picornaviruses, Noroviruses, and Coronaviruses. J.Virol. (2012)

Release Date

2012-09-05

Peptides

Genome polyprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Genome polyprotein