9MFZ | pdb_00009mfz

Streptavidin-E101Q-K121A-L124E bound to Fe(III)-biotin-pentyl-dipicolylamine cofactor

PDB DOI: https://doi.org/10.2210/pdb9MFZ/pdb

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

Deposited: 2024-12-10 Released: 2025-12-17
Deposition Author(s): Biswas, A., Follmer, A.H., Borovik, A.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.189 (Depositor), 0.189 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Streptavidin-L124E bound to Fe(III)-biotin-pentyl-dipicolylamine cofactor

Follmer, A.H., Biswas, A., Borovik, A.S.

To be published.

Macromolecule Content

Total Structure Weight: 55.54 kDa
Atom Count: 4,452
Modeled Residue Count: 500
Deposited Residue Count: 500
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	125	Streptomyces avidinii	Mutation(s): 3
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BLH (Subject of Investigation/LOI) Query on A1BLH Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], G [auth B], K [auth C], N [auth D]	N-(5-{bis[(pyridin-2-yl)methyl]amino}pentyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide C₂₇ H₃₈ N₆ O₂ S WXSQDQBSLPVFPS-GNKBHMEESA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain N [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain R [auth D] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D]	M [auth C], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain M [auth C] Focus chain R [auth D]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	F [auth A] H [auth B] I [auth B] J [auth B] L [auth C] F [auth A], H [auth B], I [auth B], J [auth B], L [auth C], O [auth D], P [auth D], Q [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D]