MolNFT v1 · #171686 · protein

Crystal structure of YTHDC1 S378A mutant

6ZD4 · Yth domain containing 1: “Crystal structure of YTHDC1 S378A mutant”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.72). MolNFT v1 #171686 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZD4
Type: protein
Length: 319 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain containing 1
Ligands: SO4
Pockets: 5 · best druggability 0.72

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yth domain containing 1	protein	155	33% helix, 26% strand	—
B	Yth domain containing 1	protein	164	33% helix, 25% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, B

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

Pockets

5 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	187	0.72	0.89	31	SO4
2	124	0.54	0.82	16	empty
3	94	0.39	0.76	17	empty
4	60	0.28	0.73	13	empty
5	56	0.27	0.74	16	empty

Interfaces

1 interface between chains.

A–B · 605 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6ZD4 · Crystal structure of YTHDC1 S378A mutant · 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
Elsewhere: RCSB PDB 6ZD4 · PDBe 6ZD4

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