8C3B | pdb_00008c3b

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

PDB DOI: https://doi.org/10.2210/pdb8C3B/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Bos taurus
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: 1.24 Å
R-Value Free:
0.227 (Depositor), 0.230 (DCC)
R-Value Work:
0.192 (Depositor), 0.200 (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: 28.26 kDa
Atom Count: 2,369
Modeled Residue Count: 248
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A [auth AAA], B [auth BBB]	124	Bos taurus	Mutation(s): 0 EC: 4.6.1.18
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823 Go to UniProtKB: P61823
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61823
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T9L (Subject of Investigation/LOI) Query on T9L Download Ideal Coordinates CCD File SDF format, chain E [auth BBB] MOL2 format, chain E [auth BBB] mmCIF format, chain E [auth BBB]	E [auth BBB]	(1,3-dimethylimidazol-1-ium-2-yl)-tetrakis(oxidanyl)ruthenium C₅ H₁₂ N₂ O₄ Ru GBFAIMOOTSOZCZ-UHFFFAOYSA-J		Interactions Focus chain E [auth BBB] Interactions & Density Focus chain E [auth BBB]
R6U (Subject of Investigation/LOI) Query on R6U Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA]	(1,3-dimethylimidazol-1-ium-2-yl)-tris(oxidanyl)ruthenium C₅ H₁₁ N₂ O₃ Ru NXUITYSMOYFBJL-UHFFFAOYSA-K		Interactions Focus chain D [auth AAA] Interactions & Density Focus chain D [auth AAA]
T9U (Subject of Investigation/LOI) Query on T9U Download Ideal Coordinates CCD File SDF format, chain F [auth BBB] MOL2 format, chain F [auth BBB] mmCIF format, chain F [auth BBB]	F [auth BBB]	(1,3-dimethyl-2~{H}-imidazol-2-yl)-oxidanyl-oxidanylidene-ruthenium C₅ H₁₀ N₂ O₂ Ru DEXKHQIKGXONQU-UHFFFAOYSA-M		Interactions Focus chain F [auth BBB] Interactions & Density Focus chain F [auth BBB]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]