MolNFT v1 · #164540 · protein

Crystal structure of YTHDC1 with fragment 29 (DHU_DC1_218)

6T11: “Crystal structure of YTHDC1 with fragment 29 (DHU_DC1_218)”. X-ray diffraction, 2 ligands (O2A, SO4), 9 pockets (best druggability 0.55). MolNFT v1 #164540 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6T11
Type: protein
Length: 325 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: O2A, SO4
Pockets: 9 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	161	34% helix, 25% strand	Q96MU7
B	YTHDC1	protein	164	32% helix, 26% strand	Q96MU7

Ligands and binding sites

O2A · N-methyl-1H-indole-7-carboxamide · ligand · chains B
SO4 · Sulfate ion · ion · 8 copies · chains A, B

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

Pockets

9 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	146	0.55	0.81	16	O2A
2	141	0.51	0.80	17	empty
3	84	0.47	0.81	18	empty
4	112	0.44	0.78	16	empty
5	97	0.40	0.77	17	empty

Interfaces

1 interface between chains.

A–B · 257 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6T11 · Crystal structure of YTHDC1 with fragment 29 (DHU_DC1_218) · 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 6T11 · PDBe 6T11 · UniProt Q96MU7

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