Research workbench
Structure of yeast RMD9P in complex with 20NT target RNA
Analyse Structure of yeast RMD9P in complex with 20NT target RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A9W
- Type
- protein + RNA
- Length
- 529 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein RMD9, mitochondrial; RNA (5'-R(*AP*UP*AP*AP*AP*AP*UP*AP*AP*CP*AP*UP*UP*CP*UP*U)…
- UniProt
- P53140
- Ligands
- CL
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein RMD9, mitochondrial | protein | 513 | 73% helix, 0% strand | P53140 |
| B | RNA (5'-R(*AP*UP*AP*AP*AP*AP*UP*AP*AP*CP*AP*UP*UP*CP*UP*U)- 3') | rna | 16 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.69 | 0.81 | 44 | empty |
| 2 | 200 | 0.49 | 0.76 | 31 | empty |
| 3 | 68 | 0.36 | 0.77 | 13 | empty |
| 4 | 72 | 0.33 | 0.75 | 22 | empty |
| 5 | 90 | 0.33 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2280 Ų buried · 49 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
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 P53140
- Elsewhere: RCSB PDB 7A9W · PDBe 7A9W · UniProt P53140
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