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Structure of yth-YTHDF2 in the free state

Analyse Structure of yth-YTHDF2 in the free state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RDO
Type: protein
Length: 870 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain-containing family protein 2
UniProt: Q9Y5A9
Ligands: SO4
Pockets: 8 · best druggability 0.64

Structure

x-ray diffraction · 6 distinct chains · 30% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yth domain-containing family protein 2	protein	149	31% helix, 30% strand	Q9Y5A9
B	Yth domain-containing family protein 2	protein	146	29% helix, 30% strand	Q9Y5A9
C	Yth domain-containing family protein 2	protein	148	29% helix, 30% strand	Q9Y5A9
D	Yth domain-containing family protein 2	protein	146	31% helix, 30% strand	Q9Y5A9
E	Yth domain-containing family protein 2	protein	141	33% helix, 31% strand	Q9Y5A9
F	Yth domain-containing family protein 2	protein	140	30% helix, 30% strand	Q9Y5A9

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	601	0.64	0.75	40	empty
2	411	0.61	0.76	33	empty
3	398	0.58	0.75	43	empty
4	222	0.55	0.78	32	empty
5	235	0.48	0.74	28	empty

Interfaces

6 interfaces between chains.

A–E · 540 Å² buried · 6 hydrogen bonds · protein-protein
C–F · 504 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 461 Å² buried · 10 hydrogen bonds · protein-protein
A–F · 284 Å² buried · 6 hydrogen bonds · protein-protein
C–E · 272 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4RDO · Structure of YTH-YTHDF2 in the free state · the same entry in another collection · chain F against F, TM-score 1.00
Q9Y5A9 · AlphaFold monomer V2.0 prediction for yth domain-containing family protein 2 (Q9Y5A9) · a predicted model of the same protein · chain F against A, TM-score 0.97

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 Q9Y5A9
Elsewhere: RCSB PDB 4RDO · PDBe 4RDO · UniProt Q9Y5A9

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