SMTL ID : 6p6l.1

HCV NS3/4A protease domain of genotype 1a in complex with glecaprevir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: K.10, T.59, T.61, Q.62, R.83 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.10, A:T.61, A:R.83 Water bridges: A:T.59 EDO.2: 4 residues within 4Å: Chain A: I.56, T.63, R.130, H.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.130, A:R.130 Water bridges: A:H.131 EDO.3: 1 residues within 4Å: Chain A: R.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.140 Water bridges: A:R.140 EDO.4: 3 residues within 4Å: Chain A: R.32, K.47, N.48 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.32, A:R.32, A:N.48

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

SO4.5: 3 residues within 4Å: Chain A: Y.27, Q.29, Q.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.29 SO4.6: 6 residues within 4Å: Chain A: K.101, S.143, R.176, I.191, P.192, S.195 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.195 Water bridges: A:S.143, A:R.176, A:R.176 Salt bridges: A:R.176

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 6 residues within 4Å: Chain A: C.118, T.119, C.120, C.166, A.168, H.170 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.118, A:C.120, A:C.166, A:H.170

1 x O31: Glecaprevir(Non-covalent)

O31.8: 23 residues within 4Å: Chain A: Q.62, T.63, F.64, V.76, Y.77, H.78, G.79, V.99, D.102, R.144, I.153, L.156, K.157, G.158, S.159, S.160, F.175, R.176, A.177, A.178, V.179, S.180, D.189 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Q.62, A:F.64, A:Y.77, A:H.78, A:V.99, A:I.153, A:F.175, A:A.178, A:V.179, A:D.189 Hydrogen bonds: A:H.78, A:G.158, A:S.159, A:S.160, A:S.160, A:R.176, A:A.178, A:A.178 pi-Stacking: A:H.78 Halogen bonds: A:R.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timm, J. et al., HCV NS3/4A protease domain of genotype 1a in complex with glecaprevir. To Be Published

Release Date

2020-06-10

Peptides

Non-structural protein 4A,Serine protease NS3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 4A,Serine protease NS3

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