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Crystal structure of YTHDC1 with compound PSI_DC1_002

Analyse Crystal structure of YTHDC1 with compound PSI_DC1_002 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PJA
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: 7RE, SO4
Pockets: 8 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Yth domain-containing protein 1	protein	164	33% helix, 25% strand	Q96MU7

Ligands and binding sites

7RE · 6-methyl-3H-pyridin-2-one · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

8 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	56	0.55	0.89	16	7RE
2	70	0.48	0.84	16	7RE
3	121	0.45	0.77	15	empty
4	94	0.41	0.77	16	empty
5	52	0.37	0.80	17	SO4

Interfaces

1 interface between chains.

A–B · 258 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7PJA · Crystal structure of YTHDC1 with compound PSI_DC1_002 · 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 7PJA · PDBe 7PJA · UniProt Q96MU7

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