Research workbench
Cryo-EM structure of ephydatia fluviatilis piwia-pirna complex
Analyse Cryo-EM structure of ephydatia fluviatilis piwia-pirna complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KX7
- Type
- protein + RNA
- Length
- 736 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Piwi-a; RNA (5'-R(P*UP*CP*UP*CP*AP*GP*(OMC))-3')
- EC
- 3.1.26.-
- UniProt
- D5MRY8
- Ligands
- MG
- Pockets
- 7 · best druggability 0.71
Structure
electron microscopy · 2 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Piwi-a (EC 3.1.26.-) | protein | 729 | 28% helix, 23% strand | D5MRY8 |
| B | RNA (5'-R(P*UP*CP*UP*CP*AP*GP*(OMC))-3') | rna | 7 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.71 | 0.75 | 90 | MG |
| 2 | 391 | 0.68 | 0.81 | 47 | empty |
| 3 | 51 | 0.42 | 0.83 | 13 | empty |
| 4 | 104 | 0.41 | 0.77 | 18 | empty |
| 5 | 62 | 0.40 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1061 Ų buried · 31 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7KX7 · Cryo-EM structure of Ephydatia fluviatilis PiwiA-piRNA complex · 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 D5MRY8
- Elsewhere: RCSB PDB 7KX7 · PDBe 7KX7 · UniProt D5MRY8
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