6ZUL | pdb_00006zul

Crystal structure of dimethylated RSL in complex with cucurbit[7]uril and zinc

PDB DOI: https://doi.org/10.2210/pdb6ZUL/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Ralstonia solanacearum
Expression System: Escherichia coli
Mutation(s): No

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: 1.62 Å
R-Value Free:
0.209 (Depositor), 0.170 (DCC)
R-Value Work:
0.174 (Depositor), 0.180 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
View more details

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: 67.36 kDa
Atom Count: 5,337
Modeled Residue Count: 539
Deposited Residue Count: 540
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, B, C, D, E A, B, C, D, E, F	90	Ralstonia solanacearum	Mutation(s): 0 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 4 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] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain Y [auth E] SDF format, chain T [auth D] SDF format, chain BA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain T [auth D] MOL2 format, chain BA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Y [auth E] mmCIF format, chain T [auth D] mmCIF format, chain BA [auth F]	BA [auth F] G [auth A] L [auth B] O [auth C] T [auth D] BA [auth F], G [auth A], L [auth B], O [auth C], T [auth D], Y [auth E]	cucurbit[7]uril C₄₂ H₄₂ N₂₈ O₁₄ ZDOBFUIMGBWEAB-XGFHMVPTSA-N		Interactions Focus chain BA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth D] Focus chain Y [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Z [auth E] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain DA [auth F] SDF format, chain CA [auth F] MOL2 format, chain AA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] mmCIF format, chain AA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F]	AA [auth E] CA [auth F] DA [auth F] H [auth A] I [auth A] AA [auth E], CA [auth F], DA [auth F], H [auth A], I [auth A], M [auth B], N [auth B], P [auth C], Q [auth C], V [auth D], W [auth D], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain X [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C]	R [auth C], S [auth C], U [auth D], X [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain X [auth D] Interactions & Density Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain X [auth D]