MolNFT v1 · #164510 · protein

Crystal structure of YTHDC1 with fragment 19 (DHU_DC1_045)

6T06: “Crystal structure of YTHDC1 with fragment 19 (DHU_DC1_045)”. X-ray diffraction, 2 ligands (M5H, SO4), 7 pockets (best druggability 0.54). MolNFT v1 #164510 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6T06
Type: protein
Length: 319 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: M5H, SO4
Pockets: 7 · best druggability 0.54

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	155	35% helix, 26% strand	Q96MU7
B	YTHDC1	protein	164	31% helix, 26% strand	Q96MU7

Ligands and binding sites

M5H · 3-imidazolidin-2-yl-2~{H}-indazole · ligand · chains B
SO4 · Sulfate ion · ion · 5 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	121	0.54	0.82	18	M5H, SO4
2	96	0.49	0.81	17	empty
3	116	0.44	0.77	15	empty
4	100	0.42	0.77	17	empty
5	91	0.38	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 255 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6T06 · Crystal structure of YTHDC1 with fragment 19 (DHU_DC1_045) · 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 6T06 · PDBe 6T06 · UniProt Q96MU7

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