Research workbench

Crystal structure of YTHDC1 with fragment 26 (DHU_DC1_198)

Analyse Crystal structure of YTHDC1 with fragment 26 (DHU_DC1_198) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T0C
Type: protein
Length: 324 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: M4E, SO4
Pockets: 7 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	162	32% helix, 26% strand	Q96MU7
B	YTHDC1	protein	162	29% helix, 28% strand	Q96MU7

Ligands and binding sites

M4E · ~{N}-methyl-2~{H}-indazole-3-carboxamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	220	0.62	0.82	31	M4E
2	89	0.52	0.83	17	M4E
3	142	0.45	0.76	18	empty
4	81	0.43	0.79	17	empty
5	95	0.40	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 261 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6T0C · Crystal structure of YTHDC1 with fragment 26 (DHU_DC1_198) · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q96MU7
Elsewhere: RCSB PDB 6T0C · PDBe 6T0C · UniProt Q96MU7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.