SMTL ID : 7m1v.1

Structure of Zika virus NS2b-NS3 protease mutant binding the compound NSC86314 in the super-open conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

1 x YO1: 4-(2-{2,4-diamino-5-[2-(4-{[(2E)-1,3-thiazolidin-2-ylidene]sulfamoyl}phenyl)hydrazinyl]phenyl}hydrazinyl)-N-[(2S)-1,3-thiazolidin-2-yl]benzene-1-sulfonamide(Non-covalent)

YO1.1: 12 residues within 4Å: Chain A: W.131, K.135, Q.136, L.138, P.144, W.145, L.147, A.149, D.182, V.208, G.210, V.217 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.138 Hydrogen bonds: A:W.145 Water bridges: A:N.214, A:N.214, A:N.214, A:N.214, B:K.135, B:K.135 pi-Stacking: A:W.131, A:W.131, A:W.145, A:W.145, A:W.145 pi-Cation interactions: A:K.135

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

EDO.2: 4 residues within 4Å: Chain A: C.150, D.152, R.207, C.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.207 Water bridges: A:C.150 EDO.4: 7 residues within 4Å: Chain B: Y.192, P.193, A.194, G.195, T.196, S.197, Y.212 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.195, B:T.196, B:S.197 Water bridges: B:H.113, B:Y.192, B:Y.192 EDO.6: 6 residues within 4Å: Chain A: H.113, D.137 Chain B: K.135, Q.136, N.214, G.215 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.113, B:N.214, B:G.215

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: A.187, V.188, G.213, G.215 Ligand excluded by PLIP

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

DMS.5: 4 residues within 4Å: Chain B: W.131, Q.136, L.138, W.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.136 pi-Cation interactions: B:W.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aleshin, A.E. et al., To be provided. To Be Published

Release Date

2021-04-21

Peptides

Core protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Core protein