MolNFT v1 · #142855 · protein + RNA
Cryo-EM structure of human ribonuclease P with mature tRNA
6AHU · H1 RNA: “Cryo-EM structure of human ribonuclease P with mature tRNA”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.88). MolNFT v1 #142855 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AHU
- Type
- protein + RNA
- Length
- 3,008 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H1 RNA; Ribonucleases P/MRP protein subunit POP1; Ribonuclease P protein subunit P38…
- EC
- 3.1.26.5
- UniProt
- Q99575, P78345, O95707, Q969H6, Q9BUL9, O75817, O95059, P78346, Q9H633, O75818
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 13 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H1 RNA | rna | 341 | — | — |
| B | Ribonucleases P/MRP protein subunit POP1 (EC 3.1.26.5) | protein | 774 | 33% helix, 16% strand | Q99575 |
| C | Ribonuclease P protein subunit P38 (EC 3.1.26.5) | protein | 182 | 22% helix, 15% strand | P78345 |
| D | Ribonuclease P protein subunit P29 (EC 3.1.26.5) | protein | 145 | 19% helix, 22% strand | O95707 |
| E | Ribonuclease P/MRP protein subunit POP5 (EC 3.1.26.5) | protein | 147 | 46% helix, 18% strand | Q969H6 |
| F | Ribonuclease P protein subunit P25 (EC 3.1.26.5) | protein | 129 | 23% helix, 32% strand | Q9BUL9 |
| G | Ribonuclease P protein subunit P20 (EC 3.1.26.5) | protein | 131 | 22% helix, 21% strand | O75817 |
| H | Ribonuclease P protein subunit P14 (EC 3.1.26.5) | protein | 121 | 24% helix, 26% strand | O95059 |
| I | Ribonuclease P protein subunit P30 (EC 3.1.26.5) | protein | 236 | 37% helix, 12% strand | P78346 |
| J | Ribonuclease P protein subunit P30 (EC 3.1.26.5) | protein | 247 | 35% helix, 14% strand | P78346 |
| K | Ribonuclease P protein subunit P21 (EC 3.1.26.5) | protein | 121 | 44% helix, 12% strand | Q9H633 |
| L | Ribonuclease P protein subunit P40 (EC 3.1.26.5) | protein | 362 | 20% helix, 33% strand | O75818 |
| T | TRNA | rna | 72 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.88 | 0.89 | 119 | empty |
| 2 | 528 | 0.84 | 0.91 | 55 | empty |
| 3 | 903 | 0.83 | 0.85 | 92 | empty |
| 4 | 828 | 0.83 | 0.86 | 64 | empty |
| 5 | 341 | 0.82 | 0.92 | 55 | empty |
Interfaces
35 interfaces between chains.
- A–B · 6299 Ų buried · 122 hydrogen bonds · protein-nucleic
- H–L · 2381 Ų buried · 20 hydrogen bonds · protein-protein
- C–K · 1864 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 1738 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–K · 1706 Ų buried · 30 hydrogen bonds · protein-nucleic
Compared structures
- 6AHU · Cryo-EM structure of human Ribonuclease P with mature tRNA · the same entry in another collection · chain T against T, TM-score 1.00
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 Q99575
- Every structure of UniProt P78345
- Every structure of UniProt O95707
- Every structure of UniProt Q969H6
- Every structure of UniProt Q9BUL9
- Every structure of UniProt O75817
- Every structure of UniProt O95059
- Every structure of UniProt P78346
- Every structure of UniProt Q9H633
- Every structure of UniProt O75818
- Elsewhere: RCSB PDB 6AHU · PDBe 6AHU · UniProt Q99575 · UniProt P78345 · UniProt O95707 · UniProt Q969H6 · UniProt Q9BUL9 · UniProt O75817 · UniProt O95059 · UniProt P78346 · UniProt Q9H633 · UniProt O75818
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