9F4M

UP1 in complex with Z1401276297

PDB DOI: https://doi.org/10.2210/pdb9F4M/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-28 Released: 2024-05-15
Deposition Author(s): Dunnett, L., Prischi, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.231
R-Value Work: 0.205
R-Value Observed: 0.206

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Enhanced identification of small molecules binding to hnRNP A1 via in silico hotspot and cryptic pockets mapping coupled with X-Ray fragment screening

Dunnett, L., Prischi, F.

To be published.

Macromolecule Content

Total Structure Weight: 22.56 kDa
Atom Count: 1,588
Modelled Residue Count: 167
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed	A	198	Homo sapiens	Mutation(s): 0 Gene Names: HNRNPA1, HNRPA1
UniProt & NIH Common Fund Data Resources
Find proteins for P09651 (Homo sapiens) Explore P09651 Go to UniProtKB: P09651
PHAROS: P09651 GTEx: ENSG00000135486
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09651
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H97 (Subject of Investigation/LOI) Query on A1H97 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(5~{R})-7-pyrazin-2-yl-2-oxa-7-azaspiro[4.4]nonane C₁₁ H₁₅ N₃ O ITTBXBSSJHVWJS-LLVKDONJSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.231
R-Value Work: 0.205
R-Value Observed: 0.206
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.994	α = 90
b = 44.09	β = 94.17
c = 55.983	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-05-15
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.