6AVK

Streptavidin bound to peptide-like compound KPM-6

• PDB DOI: https://doi.org/10.2210/pdb6AVK/pdb

• Classification: BIOTIN BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Mutation(s): No 


• Deposited: 2017-09-02 Released: 2018-08-08 
• Deposition Author(s): Park, H., Shamim, R., McEnaney, P., Kodadek, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.186 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Literature

Efficient Workflow for Screening DNA-encoded One Bead One Compound Libraries Using a Flow Cytometer

McEnaney, P., Dickson, P., Dang, V., MacConnell, A., Cavett, V., Reza, S., Park, H., Paegel, B., Kodadek, T.

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)

Macromolecule Content

• Total Structure Weight: 26.81 kDa 
• Atom Count: 2,242 
• Modelled Residue Count: 242 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B	123	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BZ4	C [auth A]	N-[(2H-1,3-benzodioxol-5-yl)methyl]-2-({[(2H-1,3-benzodioxol-5-yl)methyl][2-(chloromethyl)-1,3-oxazole-4-carbonyl]amino}methyl)-N-[(4-carbamoyl-1,3-oxazol-2-yl)methyl]-1,3-oxazole-4-carboxamide C31 H25 Cl N6 O10 ZSCMZNFJKJBCQT-UHFFFAOYSA-N
HDO	D [auth B]	1-hydroxydodecan-4-one C12 H24 O2 ZWRNUBJKJQOMRO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.186 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.31	α = 90
b = 93.52	β = 90
c = 104.45	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Park, H., Shamim, R., McEnaney, P., Kodadek, T.

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description