Macromolecule Content

Total Structure Weight: 43.14 kDa
Atom Count: 2796
Residue Count: 328
Unique protein chains: 1

6ZD5

Crystal structure of YTHDC1 S378A mutant complex with m6A

DOI: 10.2210/pdb6ZD5/pdb

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

Deposited: 2020-06-13 Released: 2021-01-13
Deposition Author(s): Bedi, R.K., Li, Y., Caflisch, A.
Funding Organization(s): Swiss National Science Foundation, Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.233
R-Value Work: 0.186
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Literature

Crystal structure of YTHDC1 with compound DHU_DC1_135

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

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain containing 1	A, B	183	Homo sapiens	Mutation(s): 0 Gene Names: YTHDC1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6MD Query on 6MD Download Ideal Coordinates CCD File SDF format, chain H [A] SDF format, chain K [B] MOL2 format, chain H [A] MOL2 format, chain K [B]	A, B	N-methyladenosine C₁₁ H₁₅ N₅ O₄ VQAYFKKCNSOZKM-IOSLPCCCSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [A] SDF format, chain E [A] SDF format, chain F [A] SDF format, chain G [A] SDF format, chain I [B] SDF format, chain J [B] MOL2 format, chain C [A] MOL2 format, chain D [A] MOL2 format, chain E [A] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain I [B] MOL2 format, chain J [B]	A, B	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.233
R-Value Work: 0.186
R-Value Observed: 0.188
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.82	α = 90
b = 103.4	β = 105.765
c = 42.49	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-06-13
Released Date: 2021-01-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B_189363
Swedish Research Council	Sweden	VR 2019-00608

Revision History

Version 1.0: 2021-01-13
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.