6YL0 | pdb_00006yl0

Crystal structure of YTHDC1 with compound T_96

• PDB DOI: https://doi.org/10.2210/pdb6YL0/pdb

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


• Deposited: 2020-04-06 Released: 2020-07-15 
• Deposition Author(s): Bedi, R.K., Huang, D., Wiedmer, L., Caflisch, A.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of YTHDC1 with compound T_96

Bedi, R.K., Huang, D., Wiedmer, L., Caflisch, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 43.11 kDa 
• Atom Count: 3,328 
• Modeled Residue Count: 330 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTHDC1	A, B	183	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MU7 (Homo sapiens) Explore Q96MU7  Go to UniProtKB:  Q96MU7
PHAROS:  Q96MU7 GTEx:  ENSG00000083896

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OWH (Subject of Investigation/LOI)	C [auth A], J [auth B]	~{N}-methylpyridine-3-carbothioamide C7 H8 N2 S FDIVIVQWGKEWIT-UHFFFAOYSA-N
PEG	I [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.53	α = 90
b = 103.07	β = 105.388
c = 42.11	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Bedi, R.K., Huang, D., Wiedmer, L., Caflisch, A.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B_189363

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description