MolNFT v1 · #164470 · protein

Crystal structure of YTHDC1 with fragment 1 (DHU_DC1_141)

6SYZ · Yth domain-containing protein 1: “Crystal structure of YTHDC1 with fragment 1 (DHU_DC1_141)”. X-ray diffraction, 2 ligands (M1E, SO4), 6 pockets (best druggability 0.57). MolNFT v1 #164470 on GenesisL1: 3D structure, binding sites…

PDB: 6SYZ
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: M1E, SO4
Pockets: 6 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Yth domain-containing protein 1	protein	164	33% helix, 24% strand	Q96MU7

Ligands and binding sites

M1E · ~{N}-methylthieno[3,2-d]pyrimidin-4-amine · ligand · 2 copies · chains A, 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

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	55	0.57	0.90	16	M1E
2	59	0.49	0.85	13	M1E
3	76	0.49	0.83	17	empty
4	98	0.45	0.79	15	empty
5	82	0.38	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 277 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6SYZ · Crystal structure of YTHDC1 with fragment 1 (DHU_DC1_141) · 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 6SYZ · PDBe 6SYZ · UniProt Q96MU7

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