6ZFC | pdb_00006zfc

Fucose-binding lectin from Burkholderia ambifaria (BamBL) in complex with a fucosyl derivative

PDB DOI: https://doi.org/10.2210/pdb6ZFC/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Burkholderia ambifaria AMMD
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-06-17 Released: 2020-10-28
Deposition Author(s): Kuhaudomlarp, S., Gillon, E., Fragai, M., Cerofolini, L., Giuntini, S., Denis, M., Santarsia, S., Valori, C., Dondoni, A., Fallarini, S., Lombardi, G., Nativi, C., Imberty, A.
Funding Organization(s): French National Research Agency, Italian Ministry of Education

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.208 (Depositor), 0.220 (DCC)
R-Value Work:
0.177 (Depositor), 0.190 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Fucosylated ubiquitin and orthogonally glycosylated mutant A28C: conceptually new ligands for Burkholderia ambifaria lectin (BambL).

Kuhaudomlarp, S., Cerofolini, L., Santarsia, S., Gillon, E., Fallarini, S., Lombardi, G., Denis, M., Giuntini, S., Valori, C., Fragai, M., Imberty, A., Dondoni, A., Nativi, C.

(2020) Chem Sci 11: 12662-12670

PubMed: 34094460 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/d0sc03741a
Primary Citation of Related Structures:
6ZFC

PubMed Abstract:
Two orthogonal, metal free click reactions, enabled to glycosylate ubiquitin and its mutant A28C forming two protein scaffolds with high affinity for BambL, a lectin from the human pathogen Burkholderia ambifaria . A new fucoside analogue, with high affinity with BambL, firstly synthetized and co-crystallized with the protein target, provided the insights for sugar determinants grafting onto ubiquitin. Three ubiquitin-based glycosides were thus assembled. Fuc-Ub , presented several copies of the fucoside analogue, with proper geometry for multivalent effect; Rha-A28C , displayed one thio-rhamnose, known for its ability to tuning the immunological response; finally, Fuc-Rha-A28C , included both multiple fucoside analogs and the rhamnose residue. Fuc-Ub and Fuc-Rha-A28C ligands proved high affinity for BambL and unprecedented immune modulatory properties towards macrophages activation.

Organizational Affiliation

Université Grenoble Alpes, CNRS, CERMAV 38000 Grenoble France.

Macromolecule Content

Total Structure Weight: 60.76 kDa
Atom Count: 4,718
Modelled Residue Count: 522
Deposited Residue Count: 522
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
bacterial lectin from Burkholderia ambifaria	A, B, C, D, E A, B, C, D, E, F	87	Burkholderia ambifaria AMMD	Mutation(s): 0 Gene Names: Bamb_5415
UniProt
Find proteins for Q0B4G1 (Burkholderia ambifaria (strain ATCC BAA-244 / DSM 16087 / CCUG 44356 / LMG 19182 / AMMD)) Explore Q0B4G1 Go to UniProtKB: Q0B4G1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0B4G1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QJB (Subject of Investigation/LOI) Query on QJB 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 J [auth B] SDF format, chain K [auth C] 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 P [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] 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 P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] 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 P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F]	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], Q [auth F], R [auth F]	2-[(2~{S},3~{S},4~{R},4~{a}~{S},10~{a}~{S})-2-methyl-3,4-bis(oxidanyl)-3,4,4~{a},10~{a}-tetrahydro-2~{H}-pyrano[2,3-b][1,4]benzoxathiin-7-yl]-~{N}-(3-oxidanylpropyl)ethanamide C₁₇ H₂₃ N O₆ S REDZBLYPLDKUEX-SSFHUKSJSA-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 Q [auth F] Focus chain R [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 Q [auth F] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.208 (Depositor), 0.220 (DCC)
R-Value Work: 0.177 (Depositor), 0.190 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.092	α = 90
b = 49.163	β = 91.36
c = 115.098	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-10-28

Deposition Author(s):

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-AAPG-2017
French National Research Agency	France	ANR-15-IDEX02
French National Research Agency	France	ANR-17-EURE-0003
Italian Ministry of Education	Italy	PRIN 2015
Italian Ministry of Education	Italy	Progetto Dipartimenti di Eccellenza 2018-2022

Revision History (Full details and data files)

Version 1.0: 2020-10-28
Type: Initial release
Version 1.1: 2021-06-23
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description