SMTL ID : 3vb3.1

Crystal structure of SARS-CoV 3C-like protease in apo form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 7 residues within 4Å: Chain A: R.4, K.5, Y.126, Q.127 Chain B: K.5, Y.126, Q.127 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.4, A:K.5, A:Q.127, B:Q.127

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: R.131, K.137, E.288, D.289, E.290 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.131, A:K.137, A:D.289, A:D.289 Water bridges: A:E.290 EDO.3: 4 residues within 4Å: Chain A: R.105, H.134, Y.182, G.183 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.105, A:R.105, A:H.134, A:G.183 EDO.4: 6 residues within 4Å: Chain A: C.22, G.23, T.24, I.43, T.45, K.61 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.24, A:K.61, A:K.61 EDO.5: 5 residues within 4Å: Chain A: T.35, H.80, S.81, R.88, K.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.35, A:S.81, A:R.88 EDO.6: 6 residues within 4Å: Chain A: N.133, H.134, P.184, F.185, A.194, G.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.195 EDO.7: 3 residues within 4Å: Chain B: L.271, I.286, L.287 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.271, B:L.287 EDO.8: 5 residues within 4Å: Chain B: N.133, P.184, F.185, A.194, G.195 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chuck, C.P. et al., Design, synthesis and crystallographic analysis of nitrile-based broad-spectrum peptidomimetic inhibitors for coronavirus 3C-like proteases. Eur.J.Med.Chem. (2012)

Release Date

2012-12-12

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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