MolNFT v1 · #185195 · protein
Crystal structure of YTHDC1 with compound PSI_DC1_004
7PJB · Yth domain-containing protein 1: “Crystal structure of YTHDC1 with compound PSI_DC1_004”. X-ray diffraction, 2 ligands (7RX, SO4), 6 pockets (best druggability 0.58). MolNFT v1 #185195 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7PJB
- Type
- protein
- Length
- 326 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yth domain-containing protein 1
- UniProt
- Q96MU7
- Ligands
- 7RX, 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 | 164 | 35% helix, 26% strand | Q96MU7 |
| B | Yth domain-containing protein 1 | protein | 162 | 31% helix, 27% strand | Q96MU7 |
Ligands and binding sites
- 7RX · (R)-homoproline · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · chains 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 | 115 | 0.58 | 0.85 | 18 | 7RX, SO4 |
| 2 | 169 | 0.55 | 0.80 | 28 | 7RX, SO4 |
| 3 | 79 | 0.45 | 0.80 | 17 | empty |
| 4 | 104 | 0.43 | 0.77 | 17 | empty |
| 5 | 101 | 0.39 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 271 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7PJB · Crystal structure of YTHDC1 with compound PSI_DC1_004 · 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 7PJB · PDBe 7PJB · UniProt Q96MU7
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