MolNFT v1 · #171687 · protein
Crystal structure of YTHDC1 S378A mutant complex with M6A
6ZD5 · Yth domain containing 1: “Crystal structure of YTHDC1 S378A mutant complex with M6A”. X-ray diffraction, 2 ligands (6MD, SO4), 4 pockets (best druggability 0.73). MolNFT v1 #171687 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ZD5
- Type
- protein
- Length
- 328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yth domain containing 1
- Ligands
- 6MD, SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Yth domain containing 1 | protein | 164 | 30% helix, 25% strand | — |
Ligands and binding sites
- 6MD · N-methyladenosine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.73 | 0.87 | 32 | SO4 |
| 2 | 81 | 0.53 | 0.85 | 16 | 6MD |
| 3 | 70 | 0.53 | 0.86 | 20 | 6MD |
| 4 | 77 | 0.39 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 552 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6ZD5 · Crystal structure of YTHDC1 S378A mutant complex with m6A · 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
- Elsewhere: RCSB PDB 6ZD5 · PDBe 6ZD5
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