MolNFT v1 · #164472 · protein

Crystal structure of YTHDC1 with fragment 2 (DHU_DC1_140)

6SZ1 · Yth domain-containing protein 1: “Crystal structure of YTHDC1 with fragment 2 (DHU_DC1_140)”. X-ray diffraction, 2 ligands (M0W, SO4), 6 pockets (best druggability 0.55). MolNFT v1 #164472 on GenesisL1: 3D structure, binding sites…

PDB: 6SZ1
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: M0W, SO4
Pockets: 6 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Yth domain-containing protein 1	protein	164	32% helix, 24% strand	Q96MU7

Ligands and binding sites

M0W · ~{N}-methylquinazolin-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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	76	0.55	0.87	19	M0W
2	57	0.55	0.88	15	M0W
3	115	0.50	0.80	16	empty
4	77	0.46	0.82	16	empty
5	89	0.38	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 304 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6SZ1 · Crystal structure of YTHDC1 with fragment 2 (DHU_DC1_140) · 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 6SZ1 · PDBe 6SZ1 · UniProt Q96MU7

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