9FYW | pdb_00009fyw

X-ray structure of the adduct formed upon reaction of RNase A with [Ru2Cl(D-p-CNPhF)(O2CCH3)3]

PDB DOI: https://doi.org/10.2210/pdb9FYW/pdb

Classification: HYDROLASE
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2024-07-04 Released: 2024-11-27
Deposition Author(s): Teran, A., Ferraro, G., Merlino, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.214 (Depositor), 0.220 (DCC)
R-Value Work:
0.174 (Depositor), 0.184 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Exchange of equatorial ligands in protein-bound paddlewheel Ru25+ complexes: new insights from X-ray crystallography and quantum chemistry

Teran, A., Fasulo, F., Ferraro, G., Sanchez-Pelaez, A.E., Herrero, S., Pavone, M., Munoz-Garcia, A.B., Merlino, A.

(2024) Inorg Chem Front 11: 7803-7811

DOI: https://doi.org/10.1039/D4QI01846J

Macromolecule Content

Total Structure Weight: 33.66 kDa
Atom Count: 2,327
Modeled Residue Count: 248
Deposited Residue Count: 300
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A, B	150	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IHW (Subject of Investigation/LOI) Query on A1IHW Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	4-[11-(4-cyanophenyl)-1,5-bis($l^{1}-oxidanyl)-3,7-dimethyl-2,4,6,8-tetraoxa-9,11-diaza-1$l^{5},5$l^{5}-diruthenatricyclo[3.3.3.0^{1,5}]undecan-9-yl]benzenecarbonitrile C₁₉ H₂₀ N₄ O₆ Ru₂ RVPMMJARIZYFTQ-UHFFFAOYSA-L		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.214 (Depositor), 0.220 (DCC)
R-Value Work: 0.174 (Depositor), 0.184 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.62	α = 90
b = 32.74	β = 90.29
c = 72.25	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-11-27
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.