9I1O | pdb_00009i1o

The MK-RSL - sulfato-terphen[3]arene complex, C121 form

PDB DOI: https://doi.org/10.2210/pdb9I1O/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Ralstonia solanacearum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-01-16 Released: 2025-07-02
Deposition Author(s): Ifeagwu, M.C., Mockler, N.M., Crowley, P.B.
Funding Organization(s): Science Foundation Ireland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.194 (Depositor), 0.193 (DCC)
R-Value Work:
0.156 (Depositor), 0.156 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

N‐Terminal Protein Complexation and Assembly with a Triangular Sulfated Macrocycle.

Ifeagwu, M.C., Guo, L., Mockler, N.M., Dong, M., Li, C., Crowley, P.B.

(2025) Cryst Growth Des 25: 4661-4665

PubMed: 40625787 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.cgd.5c00290
Primary Citation Related Structures:
9I1N, 9I1O

PubMed Abstract:
We report two cocrystal structures of a mutant Ralstonia solanacearum lectin (RSL) in complex with the recently described sulfated terphen[3]-arene ( STP3 ). This triangular macrocycle bearing 12 sulfates exhibits interesting protein-binding modes including methionine encapsulation and insertion between surface-exposed loops. These two binding modes facilitate the overall crystal packing, which may benefit from the macrocycle rigidity. In addition to a promising tool for protein assembly and crystallization, the data have implications for lectin-heparan sulfate interactions.

Organizational Affiliation

School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland.

Macromolecule Content

Total Structure Weight: 63.48 kDa
Atom Count: 5,110
Modeled Residue Count: 546
Deposited Residue Count: 546
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin protein	A, B, C, D, E A, B, C, D, E, F	91	Ralstonia solanacearum	Mutation(s): 1 Gene Names: E7Z57_08365, HF909_06975, LBW55_09125, RUN39_v1_50103
UniProt
Find proteins for A0AAP7ZHZ3 (Ralstonia solanacearum K60) Explore A0AAP7ZHZ3 Go to UniProtKB: A0AAP7ZHZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAP7ZHZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IZO (Subject of Investigation/LOI) Query on A1IZO Download:Ideal Coordinates CCD File SDF format, chain Q [auth F] MOL2 format, chain Q [auth F] mmCIF format, chain Q [auth F]	Q [auth F]	sulfato-terphen[3]arene complex C₅₇ H₄₂ O₄₈ S₁₂ LVXLICATRYFFND-UHFFFAOYSA-N		Interactions Focus chain Q [auth F] Interactions & Density Focus chain Q [auth F]
BDF Query on BDF Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain R [auth F] SDF format, chain S [auth F] SDF format, chain P [auth E] SDF format, chain K [auth C] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] MOL2 format, chain P [auth E] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth F] mmCIF format, chain P [auth E] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], R [auth F], S [auth F]	beta-D-fructopyranose C₆ H₁₂ O₆ LKDRXBCSQODPBY-ARQDHWQXSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain R [auth F] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain R [auth F] Focus chain S [auth F]