MolNFT v1 · #184361 · protein + RNA
Structure of human mitochondrial RNase P in complex with mitochondrial pre-tRNA-tyr
7ONU · 3-hydroxyacyl-CoA dehydrogenase type-2: “Structure of human mitochondrial RNase P in complex with mitochondrial pre-tRNA-tyr”. Electron microscopy, 3 ligands (NAD, ZN, MG), 20 pockets (best druggability 0.85). MolNFT v1 #184361 on…
- PDB
- 7ONU
- Type
- protein + RNA
- Length
- 1,829 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyacyl-CoA dehydrogenase type-2; Mitochondrial ribonuclease P catalytic subunit…
- EC
- 1.1.1.35, 1.1.1.62, 1.1.1.239, 1.1.1.178, 1.1.1.53, 1.1.1.159, 3.1.26.5, 2.1.1.-, 2.1.1.218, 2.1.1.221
- UniProt
- Q99714, O15091, Q7L0Y3
- Ligands
- NAD, ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-hydroxyacyl-CoA dehydrogenase type-2 (EC 1.1.1.35, 1.1.1.62, 1.1.1.239, 1.1.1.178, 1.1.1.53, 1.1.1.159) | protein | 255 | 45% helix, 18% strand | Q99714 |
| E | Mitochondrial ribonuclease P catalytic subunit (EC 3.1.26.5) | protein | 467 | 52% helix, 10% strand | O15091 |
| F | TRNA methyltransferase 10 homolog C (EC 2.1.1.-, 2.1.1.218, 2.1.1.221) | protein | 276 | 51% helix, 12% strand | Q7L0Y3 |
| T | Mitochondrial precursor tRNA-tyr | rna | 66 | — | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · chains E
- MG · Magnesium ion · metal · chains E, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.85 | 0.86 | 56 | empty |
| 2 | 676 | 0.81 | 0.86 | 52 | empty |
| 3 | 334 | 0.81 | 0.91 | 43 | empty |
| 4 | 593 | 0.80 | 0.86 | 44 | empty |
| 5 | 446 | 0.76 | 0.85 | 56 | NAD |
Interfaces
14 interfaces between chains.
- F–T · 2884 Ų buried · 51 hydrogen bonds · protein-nucleic
- A–B · 1976 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1969 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1590 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1562 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7ONU · Structure of human mitochondrial RNase P in complex with mitochondrial pre-tRNA-Tyr · the same entry in another collection · chain T against T, TM-score 1.00
- Q99714 · AlphaFold monomer V2.0 prediction for 3-hydroxyacyl-CoA dehydrogenase type-2 (Q99714) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q7L0Y3 · AlphaFold monomer V2.0 prediction for tRNA methyltransferase 10 homolog C (Q7L0Y3) · a predicted model of the same protein · chain F against A, TM-score 0.90
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 Q99714
- Every structure of UniProt O15091
- Every structure of UniProt Q7L0Y3
- Elsewhere: RCSB PDB 7ONU · PDBe 7ONU · UniProt Q99714 · UniProt O15091 · UniProt Q7L0Y3
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