5IN2 | pdb_00005in2

Crystal structure of extra cellular Cu/Zn Superoxide Dismutase from Onchocerca volvulus at 1.5 Angstrom; Insight into novel binding site and new inhibitors

• PDB DOI: https://doi.org/10.2210/pdb5IN2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Onchocerca volvulus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-07 Released: 2017-03-29 
• Deposition Author(s): Moustafa, A., Betzel, C., Perbandt, M.
• Funding Organization(s): Minstry of Higher Education, DAAD

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.181 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of extracellular Cu/Zn Superoxide Dismutase from Onchocerca volvulus at 1.5 Angstrom; Insight into novel binding site and new inhibitors

Moustafa, A., Betzel, C., Perbandt, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.64 kDa 
• Atom Count: 1,247 
• Modeled Residue Count: 156 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular superoxide dismutase [Cu-Zn]	A	158	Onchocerca volvulus	Mutation(s): 0  Gene Names: sod-4, sod2 EC: 1.15.1.1
UniProt
Find proteins for Q07449 (Onchocerca volvulus) Explore Q07449  Go to UniProtKB:  Q07449

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
AZI	H [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.181 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.41	α = 90
b = 58.41	β = 90
c = 77.63	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Moustafa, A., Betzel, C., Perbandt, M.

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Funding Organization	Location	Grant Number
Minstry of Higher Education	Egypt	--
DAAD	Germany	--

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Data collection
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary