7WD4 | pdb_00007wd4

Crystal structure of the Ilheus virus helicase: implications for enzyme function and drug design

• PDB DOI: https://doi.org/10.2210/pdb7WD4/pdb

• Classification: HYDROLASE
• Organism(s): Ilheus virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-12-21 Released: 2023-01-25 
• Deposition Author(s): Wang, D.P., Wang, M.Y., Zhou, X., Wang, W.M., Cao, J.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.198 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Ilheus virus helicase: implications for enzyme function and drug design

Cao, J.M., Wang, W.M., Zhou, X., Wang, D.P., Wang, M.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 50.27 kDa 
• Atom Count: 4,292 
• Modeled Residue Count: 437 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 helicase	A	446	Ilheus virus	Mutation(s): 0  EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for Q32ZD7 (Ilheus virus) Explore Q32ZD7  Go to UniProtKB:  Q32ZD7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.198 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.213	α = 90
b = 112.213	β = 90
c = 76.459	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Wang, D.P., Wang, M.Y., Zhou, X., Wang, W.M., Cao, J.M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82170523
National Natural Science Foundation of China (NSFC)	China	81801858

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description