MolNFT v1 · #164478 · protein
Crystal structure of YTHDC1 with fragment 5 (DHU_DC1_066)
6SZ7 · Yth domain-containing protein 1: “Crystal structure of YTHDC1 with fragment 5 (DHU_DC1_066)”. X-ray diffraction, 2 ligands (M1Q, SO4), 6 pockets (best druggability 0.58). MolNFT v1 #164478 on GenesisL1: 3D structure, binding sites…
- PDB
- 6SZ7
- Type
- protein
- Length
- 327 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yth domain-containing protein 1
- UniProt
- Q96MU7
- Ligands
- M1Q, SO4
- Pockets
- 6 · 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 | 163 | 35% helix, 26% strand | Q96MU7 |
| B | Yth domain-containing protein 1 | protein | 164 | 32% helix, 26% strand | Q96MU7 |
Ligands and binding sites
- M1Q · 5,6,7,8-tetrahydro-4~{a}~{H}-quinazoline-2,4-dione · ligand · 2 copies · chains A, 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.58 | 0.84 | 18 | M1Q |
| 2 | 138 | 0.57 | 0.83 | 17 | M1Q |
| 3 | 78 | 0.46 | 0.81 | 18 | empty |
| 4 | 115 | 0.45 | 0.78 | 15 | empty |
| 5 | 109 | 0.43 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 234 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6SZ7 · Crystal structure of YTHDC1 with fragment 5 (DHU_DC1_066) · 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 6SZ7 · PDBe 6SZ7 · UniProt Q96MU7
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