8K2E | pdb_00008k2e

Crystal structure of YTHDC1 and Y3 complex

PDB DOI: https://doi.org/10.2210/pdb8K2E/pdb

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

Deposited: 2023-07-12 Released: 2024-07-17
Deposition Author(s): Zhang, H.L., Yang, S.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.224 (Depositor), 0.223 (DCC)
R-Value Work:
0.185 (Depositor), 0.186 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

PocketFlow is a data-and-knowledge-driven structure-based molecular generative model

Jiang, Y., Zhang, G., You, J., Zhang, H., Yao, R., Xie, H., Zhang, L., Xia, Z., Dai, M., Wu, Y., Li, L., Yang, S.

(2024) Nat Mach Intell 6: 326-337

DOI: https://doi.org/10.1038/s42256-024-00808-8

Macromolecule Content

Total Structure Weight: 37.96 kDa
Atom Count: 2,896
Modeled Residue Count: 328
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing protein 1	A [auth B], B [auth A]	165	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96MU7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VIM (Subject of Investigation/LOI) Query on VIM Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth B] mmCIF format, chain E [auth A]	C [auth B], E [auth A]	2-chloranyl-6-(4-fluoranylphenoxy)benzoic acid C₁₃ H₈ Cl F O₃ XDDFAQWRNVXRFE-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain E [auth A] Interactions & Density Focus chain C [auth B] Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain F [auth A] MOL2 format, chain D [auth B] MOL2 format, chain F [auth A] mmCIF format, chain D [auth B] mmCIF format, chain F [auth A]	D [auth B], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth B] Focus chain F [auth A] Interactions & Density Focus chain D [auth B] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.224 (Depositor), 0.223 (DCC)
R-Value Work: 0.185 (Depositor), 0.186 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.644	α = 90
b = 103.515	β = 102.425
c = 41.815	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-07-17
Type: Initial release

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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.