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Crystal structure of YTHDC1 with fragment 14 (ACA_DC1_004)

Analyse Crystal structure of YTHDC1 with fragment 14 (ACA_DC1_004) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T0O
Type: protein
Length: 326 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: M6N, SO4
Pockets: 6 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	164	34% helix, 26% strand	Q96MU7
B	YTHDC1	protein	162	31% helix, 26% strand	Q96MU7

Ligands and binding sites

M6N · 2-methyl-3~{H}-pyrido[3,4-d]pyrimidin-4-one · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 8 copies · chains A, B

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

Pockets

6 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	72	0.52	0.85	14	M6N
2	96	0.50	0.82	17	M6N
3	84	0.46	0.81	17	empty
4	109	0.45	0.78	15	empty
5	105	0.41	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 270 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6T0O · Crystal structure of YTHDC1 with fragment 14 (ACA_DC1_004) · 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 6T0O · PDBe 6T0O · UniProt Q96MU7

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