Research workbench
Crystal structure of YTHDC1 with fragment 3 (DHU_DC1_149)
Analyse Crystal structure of YTHDC1 with fragment 3 (DHU_DC1_149) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SZ2
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yth domain-containing protein 1
- UniProt
- Q96MU7
- Ligands
- M0Q, SO4
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yth domain-containing protein 1 | protein | 156 | 34% helix, 26% strand | Q96MU7 |
| B | Yth domain-containing protein 1 | protein | 164 | 31% helix, 26% strand | Q96MU7 |
Ligands and binding sites
- M0Q · ~{N}-methyl-1,6-naphthyridin-4-amine · ligand · chains B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.58 | 0.83 | 17 | M0Q |
| 2 | 84 | 0.46 | 0.81 | 17 | empty |
| 3 | 109 | 0.44 | 0.77 | 15 | empty |
| 4 | 101 | 0.40 | 0.76 | 17 | empty |
| 5 | 91 | 0.38 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 255 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6SZ2 · Crystal structure of YTHDC1 with fragment 3 (DHU_DC1_149) · 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
- Every structure of UniProt Q96MU7
- Elsewhere: RCSB PDB 6SZ2 · PDBe 6SZ2 · UniProt Q96MU7
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