6ZUM | pdb_00006zum

Crystal structure of dimethylated RSL-N23H (RSL-B3) in complex with cucurbit[7]uril and zinc

PDB DOI: https://doi.org/10.2210/pdb6ZUM/pdb

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

Deposited: 2020-07-23 Released: 2020-11-25
Deposition Author(s): Guagnini, F., Engilberge, S., Flood, R.J., Ramberg, K.O., Crowley, P.B.
Funding Organization(s): Science Foundation Ireland, Irish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.203 (Depositor), 0.170 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (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

Metal-Mediated Protein-Cucurbituril Crystalline Architectures

Guagnini, F., Engilberge, S., Flood, R.J., Ramberg, K.O., Crowley, P.B.

(2020) Cryst Growth Des

DOI: https://doi.org/10.1021/acs.cgd.0c01023

Macromolecule Content

Total Structure Weight: 11.63 kDa
Atom Count: 861
Modeled Residue Count: 89
Deposited Residue Count: 90
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin protein	A	90	Ralstonia solanacearum	Mutation(s): 1 Gene Names: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
UniProt
Find proteins for A0A0S4TLR1 (Ralstonia solanacearum) Explore A0A0S4TLR1 Go to UniProtKB: A0A0S4TLR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0S4TLR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QQ7 (Subject of Investigation/LOI) Query on QQ7 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	cucurbit[7]uril C₄₂ H₄₂ N₂₈ O₁₄ ZDOBFUIMGBWEAB-XGFHMVPTSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
BDF Query on BDF Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	beta-D-fructopyranose C₆ H₁₂ O₆ LKDRXBCSQODPBY-ARQDHWQXSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]