7QWH | pdb_00007qwh

X-ray structure of the adduct formed upon reaction of a vanadium hydroxyquinoline complex with RNase A

PDB DOI: https://doi.org/10.2210/pdb7QWH/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2022-01-25 Released: 2023-02-01
Deposition Author(s): Merlino, A., Ferraro, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.222 (Depositor), 0.242 (DCC)
R-Value Work:
0.174 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7QWH

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Interaction of VIVO-8-hydroxyquinoline species with RNase A: the effect of metal ligands in the protein adduct stabilization

Ferraro, G., Vitale, L., Sciortino, G., Pisanu, F., Garribba, E., Merlino, A.

(2023) Inorg Chem Front

DOI: https://doi.org/10.1039/D3QI01023F

Macromolecule Content

Total Structure Weight: 27.65 kDa
Atom Count: 2,305
Modeled Residue Count: 248
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61823
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I3Y (Subject of Investigation/LOI) Query on I3Y 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]	2,2-bis($l^{1}-oxidanyl)-3-oxa-1$l^{4}-aza-2$l^{4}-vanadatricyclo[6.3.1.0^{4,12}]dodeca-1(12),4,6,8,10-pentaene C₉ H₈ N O₃ V VHSPINZPWRCWRI-UHFFFAOYSA-K		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.222 (Depositor), 0.242 (DCC)
R-Value Work: 0.174 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.74	α = 90
b = 32.47	β = 90.511
c = 72.86	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-02-01
Type: Initial release
Version 1.1: 2023-08-23
Changes: Data collection, Database references
Version 1.2: 2023-09-06
Changes: Database references
Version 1.3: 2024-02-07
Changes: Refinement description
Version 1.4: 2024-10-23
Changes: Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.