SMTL ID : 7i21.1

PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with NegAcid3-Am03

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

hetero-1-1-mer

Ligands

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

DMS.1: 7 residues within 4Å: Chain B: Y.121, P.122, A.123, Y.141, Y.152 Ligands: DMS.3, 01.4 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:Y.152 DMS.2: 4 residues within 4Å: Chain B: K.45, G.46, A.47 Ligands: SO4.5 No protein-ligand interaction detected (PLIP) DMS.3: 6 residues within 4Å: Chain B: G.142, N.143, G.144, Y.152 Ligands: DMS.1, 01.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.144 DMS.6: 3 residues within 4Å: Chain B: W.60, W.74, K.160 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.160 Water bridges: B:Q.65

1 x 01: 1-[(3S)-3-(aminomethyl)pyrrolidin-1-yl]-2-[4-(hydroxymethyl)-2-methylquinolin-8-yl]ethan-1-one

01.4: 14 residues within 4Å: Chain A: G.39, D.40 Chain B: H.42, D.66, D.120, Y.121, S.126, Y.141, G.142, N.143, G.144, Y.152 Ligands: DMS.1, DMS.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.141, B:Y.152 Hydrogen bonds: B:H.42, B:D.120, B:G.142, B:N.143, B:G.144 pi-Stacking: B:Y.152 pi-Cation interactions: B:H.42

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

SO4.5: 4 residues within 4Å: Chain B: K.45, G.46, A.47 Ligands: DMS.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.45 SO4.7: 2 residues within 4Å: Chain B: P.122, A.123 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.123 Water bridges: B:G.124, B:G.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, X. et al., PanDDA analysis group deposition. To Be Published

Release Date

2025-03-05

Peptides

Serine protease subunit NS2B: A
Serine protease NS3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine protease subunit NS2B

Serine protease NS3

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