Research workbench
Human mitochondrial oligoribonuclease in complex with RNA
Analyse Human mitochondrial oligoribonuclease in complex with RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J7Z
- Type
- protein + RNA
- Length
- 323 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligoribonuclease, mitochondrial; RNA (5'-R(P*UP*U)-3')
- EC
- 3.1.-.-
- UniProt
- Q9Y3B8
- Ligands
- MG
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligoribonuclease, mitochondrial (EC 3.1.-.-) | protein | 144 | 48% helix, 23% strand | Q9Y3B8 |
| B | Oligoribonuclease, mitochondrial (EC 3.1.-.-) | protein | 177 | 51% helix, 19% strand | Q9Y3B8 |
| C | RNA (5'-R(P*UP*U)-3') | rna | 2 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.48 | 0.77 | 22 | empty |
| 2 | 92 | 0.34 | 0.75 | 16 | MG |
| 3 | 58 | 0.24 | 0.72 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1798 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 405 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 122 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 6J7Z · Human mitochondrial Oligoribonuclease in complex with RNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y3B8 · AlphaFold monomer V2.0 prediction for oligoribonuclease, mitochondrial (Q9Y3B8) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9Y3B8
- Elsewhere: RCSB PDB 6J7Z · PDBe 6J7Z · UniProt Q9Y3B8
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