Research workbench
Crystal structure of the toxoplasma CPSF4 yth-domain in complex with a 7 mer M6A-modified RNA
Analyse Crystal structure of the toxoplasma CPSF4 yth-domain in complex with a 7 mer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NJC
- Type
- protein + RNA
- Length
- 151 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc finger (ccch type) motif-containing protein; RNA (5'-R(*(6MZ)P*CP*A)-3')
- UniProt
- S8F6K2
- Ligands
- TOE, 6MD
- Pockets
- 1 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc finger (ccch type) motif-containing protein | protein | 149 | 32% helix, 34% strand | S8F6K2 |
| B | RNA (5'-R(*(6MZ)P*CP*A)-3') | rna | 2 | — | — |
Ligands and binding sites
- TOE · 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl · ligand · chains A
- 6MD · N-methyladenosine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.43 | 0.78 | 16 | 6MD |
Interfaces
1 interface between chains.
- A–B · 301 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7NJC · Crystal structure of the Toxoplasma CPSF4 YTH-domain in complex with a 7 mer m6A-modified… · 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 S8F6K2
- Elsewhere: RCSB PDB 7NJC · PDBe 7NJC · UniProt S8F6K2
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