8FHM

RNase A-Uridine 5'-Hexaphosphate (RNaseA.p6U)

PDB DOI: https://doi.org/10.2210/pdb8FHM/pdb

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

Deposited: 2022-12-14 Released: 2023-12-20
Deposition Author(s): Park, G., Cummins, C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.231
R-Value Work: 0.178
R-Value Observed: 0.181

Method: SOLUTION SCATTERING

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Pentaphosphorylation via the Anhydride of Dihydrogen Pentametaphosphate: Access to Nucleoside Hexa- and Heptaphosphates and Study of Their Interaction with Ribonuclease A

Park, G., Wralstad, E.C., Faginas-Lago, N., Qian, K., Raines, R.T., Bistoni, G., Cummins, C.C.

(2024) ACS Cent Sci

DOI: https://doi.org/10.1021/acscentsci.4c00835

Macromolecule Content

Total Structure Weight: 29.59 kDa
Atom Count: 2,313
Modelled 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, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U6F (Subject of Investigation/LOI) Query on U6F Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B]	C [auth A], D [auth B], E [auth B]	5'-O-[(S)-hydroxy{[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]uridine C₉ H₁₈ N₂ O₂₄ P₆ NJANLGXPTVMCFP-XVFCMESISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.231
R-Value Work: 0.178
R-Value Observed: 0.181
Space Group: C 1 2 1

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.069	α = 90
b = 32.527	β = 90.48
c = 72.785	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
SAINT	data reduction
SADABS	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-12-20
Type: Initial release
Version 1.1: 2024-07-24
Changes: Database references

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 R01GM133198.