6AVK | pdb_00006avk

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.186 (Depositor), 0.180 (DCC)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BZ4 Query on BZ4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
HDO Query on HDO Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	1-hydroxydodecan-4-one C₁₂ H₂₄ O₂ ZWRNUBJKJQOMRO-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.186 (Depositor), 0.180 (DCC)
R-Value Work: 0.174 (Depositor)
R-Value Observed: 0.174 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-08-08

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.