MolNFT v1 · #171690 · protein

Crystal structure of YTHDC1 T379V mutant

6ZD8: “Crystal structure of YTHDC1 T379V mutant”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.68). MolNFT v1 #171690 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZD8
Type: protein
Length: 319 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
Ligands: SO4
Pockets: 5 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	164	35% helix, 25% strand	—
B	YTHDC1	protein	155	34% helix, 26% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 9 copies · chains A, B

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

Pockets

5 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	180	0.68	0.87	30	SO4
2	77	0.51	0.84	16	empty
3	91	0.41	0.77	17	empty
4	72	0.32	0.74	24	empty
5	72	0.30	0.73	14	empty

Interfaces

1 interface between chains.

A–B · 573 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6ZD8 · Crystal structure of YTHDC1 T379V mutant · 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
Elsewhere: RCSB PDB 6ZD8 · PDBe 6ZD8

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