8AQJ

Hydrophobic probe bound to Streptavidin - 2

PDB DOI: https://doi.org/10.2210/pdb8AQJ/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Streptomyces avidinii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-08-12 Released: 2022-08-31
Deposition Author(s): Igareta, N.V., Ward, T.R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.234
R-Value Work: 0.198
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Hydrophobic probe bound to Streptavidin - 2

Igareta, N.V., Ward, T.R.

To be published.

Macromolecule Content

Total Structure Weight: 16.95 kDa
Atom Count: 1,031
Modelled Residue Count: 125
Deposited Residue Count: 158
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A	158	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629 Go to UniProtKB: P22629
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
N9O (Subject of Investigation/LOI) Query on N9O Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-[2-[6-(dimethylamino)-1,3-bis(oxidanylidene)benzo[de]isoquinolin-2-yl]ethyl]pentanamide C₂₆ H₃₁ N₅ O₄ S WAGQBAHKYBJEAZ-LEDOBFOHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.234
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.345	α = 90
b = 57.345	β = 90
c = 174.447	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-08-31
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.