Research workbench
Structure of yeast RMD9P in complex with 16NT target RNA
Analyse Structure of yeast RMD9P in complex with 16NT target RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A9X
- Type
- protein + RNA
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein RMD9, mitochondrial; RNA (5'-R(P*AP*AP*AP*UP*AP*AP*CP*AP*UP*UP*CP*UP*U)-3')
- UniProt
- P53140
- Ligands
- CL
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein RMD9, mitochondrial | protein | 513 | 72% helix, 0% strand | P53140 |
| B | RNA (5'-R(P*AP*AP*AP*UP*AP*AP*CP*AP*UP*UP*CP*UP*U)-3') | rna | 13 | — | — |
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 | 445 | 0.71 | 0.82 | 42 | empty |
| 2 | 211 | 0.48 | 0.75 | 27 | empty |
| 3 | 128 | 0.41 | 0.75 | 19 | empty |
| 4 | 62 | 0.33 | 0.77 | 21 | empty |
| 5 | 79 | 0.30 | 0.73 | 21 | CL |
Interfaces
1 interface between chains.
- A–B · 2157 Ų buried · 46 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 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 7A9X · PDBe 7A9X · UniProt P53140
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