MolNFT v1 · #105687 · protein

Crystal structure of YTHDF1 yth domain

4RCI · Yth domain-containing family protein 1: “Crystal structure of YTHDF1 yth domain”. X-ray diffraction, 1 ligand (UNX), 4 pockets (best druggability 0.78). MolNFT v1 #105687 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4RCI
Type: protein
Length: 733 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain-containing family protein 1
UniProt: Q9BYJ9
Ligands: UNX
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Yth domain-containing family protein 1	protein	183	44% helix, 24% strand	Q9BYJ9
B	Yth domain-containing family protein 1	protein	182	42% helix, 23% strand	Q9BYJ9
C	Yth domain-containing family protein 1	protein	185	43% helix, 24% strand	Q9BYJ9

Ligands and binding sites

UNX · Unknown atom or ion · ion · 57 copies · chains A, D, B, C

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1160	0.78	0.80	101	UNX
2	1121	0.77	0.79	85	UNX
3	255	0.50	0.75	35	UNX
4	197	0.49	0.76	21	UNX

Interfaces

5 interfaces between chains.

A–D · 1283 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 1190 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 225 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 118 Å² buried · 1 hydrogen bond · protein-protein
A–B · 64 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4RCI · Crystal structure of YTHDF1 YTH domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9BYJ9 · AlphaFold monomer V2.0 prediction for yth domain-containing family protein 1 (Q9BYJ9) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9BYJ9
Elsewhere: RCSB PDB 4RCI · PDBe 4RCI · UniProt Q9BYJ9

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