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Crystal structure of YTHDC1 M438A mutant

Analyse Crystal structure of YTHDC1 M438A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZD3
Type: protein
Length: 312 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 0.48

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Yth domain containing 1	protein	157	34% helix, 27% strand	—
A	Yth domain containing 1	protein	155	34% helix, 26% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains B, A
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	159	0.48	0.77	17	empty
2	92	0.45	0.80	18	empty
3	96	0.40	0.77	16	PEG
4	129	0.40	0.74	15	empty
5	54	0.29	0.75	16	empty

Interfaces

1 interface between chains.

B–A · 330 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6ZD3 · Crystal structure of YTHDC1 M438A mutant · the same entry in another collection · chain B against B, 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 6ZD3 · PDBe 6ZD3

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