MolNFT v1 · #154300 · protein

Crystal structure of the human YTHDC2 yth domain

6K6U · 3'-5' RNA helicase YTHDC2: “Crystal structure of the human YTHDC2 yth domain”. X-ray diffraction, 3 pockets (best druggability 0.53). MolNFT v1 #154300 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6K6U
Type: protein
Length: 257 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3'-5' RNA helicase YTHDC2
EC: 3.6.4.13
UniProt: Q9H6S0
Pockets: 3 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3'-5' RNA helicase YTHDC2 (EC 3.6.4.13)	protein	129	33% helix, 30% strand	Q9H6S0
B	3'-5' RNA helicase YTHDC2 (EC 3.6.4.13)	protein	128	33% helix, 30% strand	Q9H6S0

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	133	0.53	0.81	32	empty
2	63	0.29	0.74	13	empty
3	66	0.28	0.73	16	empty

Interfaces

1 interface between chains.

A–B · 414 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6K6U · Crystal structure of the human YTHDC2 YTH domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9H6S0 · AlphaFold monomer V2.0 prediction for 3'-5' RNA helicase YTHDC2 (Q9H6S0) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q9H6S0
Elsewhere: RCSB PDB 6K6U · PDBe 6K6U · UniProt Q9H6S0

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