4Y5D | pdb_00004y5d

CRYSTAL STRUCTURE OF ALiS2-STREPTAVIDIN COMPLEX

PDB DOI: https://doi.org/10.2210/pdb4Y5D/pdb

Classification: BIOTIN-BINDING PROTEIN
Organism(s): Streptomyces avidinii
Expression System: Streptomyces avidinii
Mutation(s): No

Deposited: 2015-02-11 Released: 2015-09-23
Deposition Author(s): Sugiyama, S., Terai, T., Kohno, M., Ishida, H., Nagano, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.174 (Depositor), 0.174 (DCC)
R-Value Work:
0.138 (Depositor), 0.139 (DCC)
R-Value Observed:
0.140 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Artificial Ligands of Streptavidin (ALiS): Discovery, Characterization, and Application for Reversible Control of Intracellular Protein Transport

Terai, T., Kohno, M., Boncompain, G., Sugiyama, S., Saito, N., Fujikake, R., Ueno, T., Komatsu, T., Hanaoka, K., Okabe, T., Urano, Y., Perez, F., Nagano, T.

(2015) J Am Chem Soc 137: 10464-10467

PubMed: 26261872 Search on PubMed
DOI: https://doi.org/10.1021/jacs.5b05672
Primary Citation Related Structures:
4Y59, 4Y5D

PubMed Abstract:
Artificial ligands of streptavidin (ALiS) with association constants of ∼10(6) M(-1) were discovered by high-throughput screening of our chemical library, and their binding characteristics, including X-ray crystal structure of the streptavidin complex, were determined. Unlike biotin and its derivatives, ALiS exhibits fast dissociation kinetics and excellent cell permeability. The streptavidin-ALiS system provides a novel, practical compound-dependent methodology for repeated reversible cycling of protein localization between intracellular organella.

Organizational Affiliation

Graduate School of Science, Osaka University , 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

Macromolecule Content

Total Structure Weight: 53.49 kDa
Atom Count: 4,380
Modeled Residue Count: 488
Deposited Residue Count: 488
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	122	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE3 Query on PE3 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C₂₈ H₅₈ O₁₅ ILLKMACMBHTSHP-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C]	I [auth C], J [auth C]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain I [auth C] Focus chain J [auth C]
MT6 Query on MT6 Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], K [auth D]	methyl 3-(4-oxo-4,5-dihydrofuro[3,2-c]pyridin-2-yl)benzoate C₁₅ H₁₁ N O₄ OVTGPKXYLOQTEQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth D]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]