SMTL ID : 5hyo.1

X-Ray Structure of Unbound Porcine Epidemic Diarrhea Virus 3CLpro

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

IPA.1: 1 residues within 4Å: Chain A: G.298 No protein-ligand interaction detected (PLIP) IPA.2: 2 residues within 4Å: Chain A: R.19, D.118 No protein-ligand interaction detected (PLIP) IPA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) IPA.4: 5 residues within 4Å: Chain A: R.130, R.136, S.168, C.170, E.193 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.130, A:R.130, A:E.193 IPA.5: 5 residues within 4Å: Chain A: T.35, I.37, Q.87, Y.100, Y.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.100, A:Y.100 IPA.8: 9 residues within 4Å: Chain B: K.5, M.6, Q.8, S.110, F.111, N.112, G.126, N.150, E.291 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.8 Hydrogen bonds: B:F.111 IPA.9: 4 residues within 4Å: Chain B: H.41, Q.163, Q.187 Ligands: MPD.10 No protein-ligand interaction detected (PLIP)

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 9 residues within 4Å: Chain A: M.6, Q.8, S.110, F.111, N.112, N.150, E.291, R.294, Q.295 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.8, A:E.291 Hydrogen bonds: A:R.294 MPD.10: 12 residues within 4Å: Chain A: A.1 Chain B: F.139, I.140, N.141, A.143, C.144, H.162, Q.163, L.164, E.165, H.171 Ligands: IPA.9 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.139, B:E.165 Hydrogen bonds: B:N.141, B:H.162 Water bridges: B:C.144

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 7 residues within 4Å: Chain A: F.139, I.140, A.143, C.144, H.162, L.164, E.165 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.143, A:C.144 Water bridges: A:G.142 Salt bridges: A:E.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

St John, S.E. et al., X-Ray Structure and Inhibition of 3C-like Protease from Porcine Epidemic Diarrhea Virus. Sci Rep (2016)

Release Date

2016-06-01

Peptides

PEDV 3CLpro: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PEDV 3CLpro