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Crystal structure of YTHDC1 with fragment 28 (DHU_DC1_176)

Analyse Crystal structure of YTHDC1 with fragment 28 (DHU_DC1_176) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T10
Type: protein
Length: 319 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: M6Z, SO4
Pockets: 7 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	164	34% helix, 25% strand	Q96MU7
B	YTHDC1	protein	155	33% helix, 27% strand	Q96MU7

Ligands and binding sites

M6Z · 5-iodanyl-~{N}-methyl-1~{H}-indazole-3-carboxamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 7 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	94	0.54	0.84	18	M6Z
2	88	0.45	0.80	18	empty
3	108	0.43	0.77	16	empty
4	91	0.38	0.76	16	empty
5	96	0.37	0.75	15	M6Z

Interfaces

1 interface between chains.

A–B · 252 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6T10 · Crystal structure of YTHDC1 with fragment 28 (DHU_DC1_176) · the same entry in another collection · chain A against A, TM-score 1.00

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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 6T10 · PDBe 6T10 · UniProt Q96MU7

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