MolNFT v1 · #168369 · protein

Yth domain of human YTHDC1

6WE8 · Yth domain-containing protein 1: “Yth domain of human YTHDC1”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.56). MolNFT v1 #168369 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6WE8
Type: protein
Length: 328 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain-containing protein 1
UniProt: Q96MU7
Ligands: SO4
Pockets: 8 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Yth domain-containing protein 1	protein	164	34% helix, 26% strand	Q96MU7

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains B, A
EDO · 1,2-ethanediol · additive · 8 copies · chains B, A
GOL · Glycerol · additive · chains B, A

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

Pockets

8 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	176	0.56	0.81	29	EDO
2	124	0.55	0.83	17	EDO
3	84	0.46	0.80	17	empty
4	75	0.42	0.80	15	empty
5	99	0.41	0.76	16	empty

Interfaces

1 interface between chains.

B–A · 257 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6WE8 · YTH domain of human YTHDC1 · the same entry in another collection · chain B against B, 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 6WE8 · PDBe 6WE8 · UniProt Q96MU7

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