MolNFT v1 · #164501 · protein

Crystal structure of YTHDC1 with fragment 11 (DHU_DC1_128)

6SZX: “Crystal structure of YTHDC1 with fragment 11 (DHU_DC1_128)”. X-ray diffraction, 2 ligands (M4K, SO4), 8 pockets (best druggability 0.58). MolNFT v1 #164501 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6SZX
Type: protein
Length: 325 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YTHDC1
UniProt: Q96MU7
Ligands: M4K, SO4
Pockets: 8 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTHDC1	protein	161	35% helix, 25% strand	Q96MU7
B	YTHDC1	protein	164	34% helix, 26% strand	Q96MU7

Ligands and binding sites

M4K · 6-[[cyclopropyl-(phenylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B

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

Pockets

8 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	121	0.58	0.84	18	M4K
2	129	0.57	0.83	19	M4K
3	93	0.48	0.81	16	empty
4	118	0.43	0.77	15	empty
5	108	0.42	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 250 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6SZX · Crystal structure of YTHDC1 with fragment 11 (DHU_DC1_128) · 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 6SZX · PDBe 6SZX · UniProt Q96MU7

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