9H2Y | pdb_00009h2y

Crystal structure of YTHDC1 in complex with AI_056

PDB DOI: https://doi.org/10.2210/pdb9H2Y/pdb

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

Deposited: 2024-10-15 Released: 2025-08-27
Deposition Author(s): Bedi, R.K., Caflisch, A.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.24 Å
R-Value Free:
0.243 (Depositor), 0.243 (DCC)
R-Value Work:
0.216 (Depositor), 0.215 (DCC)
R-Value Observed:
0.217 (Depositor)

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

Crystal structure of YTHDC1 in complex with AI_056

Bedi, R.K., Caflisch, A.

To be published.

Macromolecule Content

Total Structure Weight: 38.61 kDa
Atom Count: 2,850
Modeled Residue Count: 315
Deposited Residue Count: 332
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing protein 1	A, B	166	Homo sapiens	Mutation(s): 0 Gene Names: YTHDC1, KIAA1966, YT521
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MU7 (Homo sapiens) Explore Q96MU7 Go to UniProtKB: Q96MU7
PHAROS: Q96MU7 GTEx: ENSG00000083896
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96MU7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IR4 (Subject of Investigation/LOI) Query on A1IR4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	C [auth A], D [auth A], H [auth B]	3-sulfanyl-1,2,4-triazin-5-ol C₃ H₃ N₃ O S HZPZCLDCTLLJTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]