8C39 | pdb_00008c39

X-ray structure of HEWL upon reaction with a Ruthenium(II)-arene Complexed with Glycosylated Carbene Ligands (5)

PDB DOI: https://doi.org/10.2210/pdb8C39/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2022-12-23 Released: 2024-01-10
Deposition Author(s): Ferraro, G., Merlino, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.221 (Depositor), 0.229 (DCC)
R-Value Work:
0.179 (Depositor), 0.186 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Ruthenium(II)–Arene Complexes with Glycosylated NHC-Carbene Co-Ligands: Synthesis, Hydrolytic Behavior, and Binding to Biological Molecules

Annunziata, A., Cucciolito, M.E., Di Ronza, M., Ferraro, G., Hadiji, M., Merlino, A., Ortiz, D., Scopelliti, R., Fadaei Tirani, F., Dyson, P.J., Ruffo, F.

(2023) Organometallics 42: 952-964

DOI: https://doi.org/10.1021/acs.organomet.3c00128

Macromolecule Content

Total Structure Weight: 15.49 kDa
Atom Count: 1,349
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	A [auth AAA]	129	Gallus gallus	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T8K (Subject of Investigation/LOI) Query on T8K Download:Ideal Coordinates CCD File SDF format, chain O [auth AAA] MOL2 format, chain O [auth AAA] mmCIF format, chain O [auth AAA]	O [auth AAA]	[1-[(3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-3-methyl-imidazol-1-ium-2-yl]-nitrooxy-tris(oxidanyl)ruthenium C₁₀ H₁₉ N₃ O₁₁ Ru YHWXYWLAKQRSBE-BYNJHPACSA-K		Interactions Focus chain O [auth AAA] Interactions & Density Focus chain O [auth AAA]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain J [auth AAA] SDF format, chain K [auth AAA] SDF format, chain L [auth AAA] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain L [auth AAA] mmCIF format, chain C [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain L [auth AAA]	C [auth AAA] D [auth AAA] E [auth AAA] F [auth AAA] G [auth AAA] C [auth AAA], D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], L [auth AAA]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth AAA] MOL2 format, chain M [auth AAA] mmCIF format, chain M [auth AAA]	M [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth AAA] Interactions & Density Focus chain M [auth AAA]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth AAA] SDF format, chain N [auth AAA] MOL2 format, chain B [auth AAA] MOL2 format, chain N [auth AAA] mmCIF format, chain B [auth AAA] mmCIF format, chain N [auth AAA]	B [auth AAA], N [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth AAA] Focus chain N [auth AAA] Interactions & Density Focus chain B [auth AAA] Focus chain N [auth AAA]