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Crystal structure of YTHDC1 with fragment 15 (DHU_DC1_169)

Analyse Crystal structure of YTHDC1 with fragment 15 (DHU_DC1_169) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T02
Type: protein
Length: 319 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: M5E, SO4
Pockets: 6 · best druggability 0.55

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	155	34% helix, 26% strand	Q96MU7
B	YTHDC1	protein	164	32% helix, 26% strand	Q96MU7

Ligands and binding sites

M5E · (~{S})-phenyl-[(2~{S})-pyrrolidin-2-yl]methanol · ligand · 3 copies · chains A, B
SO4 · Sulfate ion · ion · 10 copies · chains A, B

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

Pockets

6 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	210	0.55	0.78	20	M5E, SO4
2	90	0.46	0.80	18	empty
3	111	0.43	0.77	17	empty
4	62	0.35	0.77	14	empty
5	97	0.34	0.74	14	M5E, SO4

Interfaces

1 interface between chains.

A–B · 252 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6T02 · Crystal structure of YTHDC1 with fragment 15 (DHU_DC1_169) · 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 6T02 · PDBe 6T02 · UniProt Q96MU7

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