8R3C | pdb_00008r3c

Cocrystal form II of the Pent - sulfonato-calix[8]arene complex

PDB DOI: https://doi.org/10.2210/pdb8R3C/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Enterobacteria phage L1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-11-08 Released: 2024-03-06
Deposition Author(s): Flood, R.J., Crowley, P.B.
Funding Organization(s): Science Foundation Ireland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.222 (Depositor), 0.222 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (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

Multivalent Calixarene Complexation of a Designed Pentameric Lectin.

Flood, R.J., Cerofolini, L., Fragai, M., Crowley, P.B.

(2024) Biomacromolecules 25: 1303-1309

PubMed: 38227741 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.biomac.3c01280
Primary Citation Related Structures:
8R3B, 8R3C, 8R3D

PubMed Abstract:
We describe complex formation between a designed pentameric β-propeller and the anionic macrocycle sulfonato-calix[8]arene ( sclx ₈), as characterized by X-ray crystallography and NMR spectroscopy. Two crystal structures and ¹⁵N HSQC experiments reveal a single calixarene binding site in the concave pocket of the β-propeller toroid. Despite the symmetry mismatch between the pentameric protein and the octameric macrocycle, they form a high affinity multivalent complex, with the largest protein-calixarene interface observed to date. This system provides a platform for investigating multivalency.

Organizational Affiliation

SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland.

Macromolecule Content

Total Structure Weight: 56.98 kDa
Atom Count: 4,290
Modeled Residue Count: 470
Deposited Residue Count: 480
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta propeller	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	48	Enterobacteria phage L1	Mutation(s): 1
UniProt
Find proteins for A0A140UHM9 (Enterobacteria phage L1) Explore A0A140UHM9 Go to UniProtKB: A0A140UHM9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A140UHM9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EVB (Subject of Investigation/LOI) Query on EVB Download:Ideal Coordinates CCD File SDF format, chain P [auth E] MOL2 format, chain P [auth E] mmCIF format, chain P [auth E]	P [auth E]	sulfonato-calix[8]arene C₅₆ H₄₈ O₃₂ S₈ KCEGJGDGMRAJEP-UHFFFAOYSA-N		Interactions Focus chain P [auth E] Interactions & Density Focus chain P [auth E]
NDG Query on NDG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth B] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain Q [auth F] SDF format, chain R [auth G] SDF format, chain S [auth H] SDF format, chain T [auth H] SDF format, chain U [auth I] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth G] MOL2 format, chain S [auth H] MOL2 format, chain T [auth H] MOL2 format, chain U [auth I] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth G] mmCIF format, chain S [auth H] mmCIF format, chain T [auth H] mmCIF format, chain U [auth I]	K [auth A] L [auth A] M [auth B] N [auth D] O [auth D] K [auth A], L [auth A], M [auth B], N [auth D], O [auth D], Q [auth F], R [auth G], S [auth H], T [auth H], U [auth I]	2-acetamido-2-deoxy-alpha-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-PVFLNQBWSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth D] Focus chain O [auth D] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth I] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth D] Focus chain O [auth D] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth I]