MolNFT v1 · #171669 · protein

Crystal structure of YTHDC1 with M6A

6ZCN: “Crystal structure of YTHDC1 with M6A”. X-ray diffraction, 2 ligands (6MZ, SO4), 7 pockets (best druggability 0.57). MolNFT v1 #171669 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZCN
Type: protein
Length: 328 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: 6MZ, SO4
Pockets: 7 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	YTHDC1	protein	164	34% helix, 24% strand	Q96MU7

Ligands and binding sites

6MZ · N6-methyladenosine-5'-monophosphate · 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	70	0.57	0.88	17	6MZ
2	80	0.51	0.84	16	6MZ
3	84	0.46	0.81	19	empty
4	114	0.43	0.77	16	empty
5	92	0.40	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 269 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6ZCN · Crystal structure of YTHDC1 with m6A · 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 6ZCN · PDBe 6ZCN · UniProt Q96MU7

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