9EC5 | pdb_00009ec5

Streptavidin-S112C-L124F bound to Cu(II)dpea cofactor, containing S-nitrosocysteine modification

• PDB DOI: https://doi.org/10.2210/pdb9EC5/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2024-11-13 Released: 2025-11-19 
• Deposition Author(s): Minnetian, N.M., Follmer, A.H., Borovik, A.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

S-nitrosylation by artificial copper metalloproteins

Minnetian, N.M., Borovik, A.S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.38 kDa 
• Atom Count: 1,156 
• Modeled Residue Count: 124 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A	159	Streptomyces avidinii	Mutation(s): 3
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BIA (Subject of Investigation/LOI)	B [auth A]	N-(3-{bis[2-(pyridin-2-yl)ethyl]amino}propyl)-5-[(3aR,4R,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide C27 H38 N6 O2 S UQOFISLZDAPJQV-DGWZTRNLSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CU (Subject of Investigation/LOI)	C [auth A], D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNC	A	L-PEPTIDE LINKING	C3 H6 N2 O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.675	α = 90
b = 57.675	β = 90
c = 183.928	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
PHASER	phasing
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Minnetian, N.M., Follmer, A.H., Borovik, A.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM120349

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release