Research workbench
Human mitochondrial oligoribonuclease in complex with DNA
Analyse Human mitochondrial oligoribonuclease in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J7Y
- Type
- protein + DNA
- Length
- 306 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligoribonuclease, mitochondrial; DNA (5'-D(P*TP*T)-3')
- EC
- 3.1.-.-
- UniProt
- Q9Y3B8
- Ligands
- MG
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Oligoribonuclease, mitochondrial (EC 3.1.-.-) | protein | 165 | 49% helix, 21% strand | Q9Y3B8 |
| A | Oligoribonuclease, mitochondrial (EC 3.1.-.-) | protein | 139 | 50% helix, 21% strand | Q9Y3B8 |
| C | DNA (5'-D(P*TP*T)-3') | dna | 2 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.34 | 0.75 | 12 | empty |
| 2 | 54 | 0.32 | 0.78 | 16 | MG |
Interfaces
3 interfaces between chains.
- B–A · 1762 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 392 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 130 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6J7Y · Human mitochondrial Oligoribonuclease in complex with DNA · the same entry in another collection · chain B against B, 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 6J7Y · PDBe 6J7Y · UniProt Q9Y3B8
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