6YL0

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.207
R-Value Work: 0.188
R-Value Observed: 0.189

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of YTHDC1 with compound T_96

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

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
GTEx: ENSG00000083896
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96MU7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OWH (Subject of Investigation/LOI) Query on OWH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B]	C [auth A], J [auth B]	~{N}-methylpyridine-3-carbothioamide C₇ H₈ N₂ S FDIVIVQWGKEWIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth B] 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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.207
R-Value Work: 0.188
R-Value Observed: 0.189
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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-07-15

Deposition Author(s):

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

Revision History (Full details and data files)

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

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Help and Resources

6YL0

Crystal structure of YTHDC1 with compound T_96

Crystal structure of YTHDC1 with compound T_96

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)