Research workbench
Cryo-EM structure of yeast ribonuclease P with pre-tRNA substrate
Analyse Cryo-EM structure of yeast ribonuclease P with pre-tRNA substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AH3
- Type
- protein + RNA
- Length
- 2,829 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease P RNA; Ribonucleases P/MRP protein subunit POP1; Ribonucleases P/MRP protein…
- EC
- 3.1.26.5
- UniProt
- P41812, P53833, P38336, P28005, P53218, P38291, P38208, P38786, P40571
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 12 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease P RNA | rna | 369 | — | — |
| B | Ribonucleases P/MRP protein subunit POP1 (EC 3.1.26.5) | protein | 784 | 38% helix, 16% strand | P41812 |
| C | Ribonucleases P/MRP protein subunit POP3 | protein | 175 | 32% helix, 22% strand | P53833 |
| D | Rnases MRP/P 32.9 kda subunit | protein | 203 | 43% helix, 18% strand | P38336 |
| E | Ribonuclease P/MRP protein subunit POP5 (EC 3.1.26.5) | protein | 146 | 42% helix, 21% strand | P28005 |
| F | Ribonucleases P/MRP protein subunit POP6 (EC 3.1.26.5) | protein | 157 | 27% helix, 34% strand | P53218 |
| G | Ribonucleases P/MRP protein subunit POP7 (EC 3.1.26.5) | protein | 121 | 25% helix, 36% strand | P38291 |
| H | Ribonucleases P/MRP protein subunit POP8 (EC 3.1.26.5) | protein | 131 | 40% helix, 24% strand | P38208 |
| I | Ribonuclease P/MRP protein subunit RPP1 (EC 3.1.26.5) | protein | 242 | 43% helix, 18% strand | P38786 |
| J | Ribonuclease P/MRP protein subunit RPP1 (EC 3.1.26.5) | protein | 293 | 38% helix, 15% strand | P38786 |
| K | Ribonuclease P protein subunit RPR2 (EC 3.1.26.5) | protein | 128 | 39% helix, 12% strand | P40571 |
| T | Pre-tRNA | rna | 80 | — | — |
Ligands and binding sites
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 | 1032 | 0.89 | 0.91 | 93 | empty |
| 2 | 948 | 0.86 | 0.88 | 79 | empty |
| 3 | 1057 | 0.84 | 0.85 | 86 | empty |
| 4 | 513 | 0.82 | 0.89 | 69 | empty |
| 5 | 467 | 0.82 | 0.90 | 51 | empty |
Interfaces
34 interfaces between chains.
- A–B · 7484 Ų buried · 123 hydrogen bonds · protein-nucleic
- A–G · 2420 Ų buried · 43 hydrogen bonds · protein-nucleic
- D–J · 2376 Ų buried · 23 hydrogen bonds · protein-protein
- C–K · 2232 Ų buried · 8 hydrogen bonds · protein-protein
- D–K · 1562 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6AH3 · Cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate · 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 P41812
- Every structure of UniProt P53833
- Every structure of UniProt P38336
- Every structure of UniProt P28005
- Every structure of UniProt P53218
- Every structure of UniProt P38291
- Every structure of UniProt P38208
- Every structure of UniProt P38786
- Every structure of UniProt P40571
- Elsewhere: RCSB PDB 6AH3 · PDBe 6AH3 · UniProt P41812 · UniProt P53833 · UniProt P38336 · UniProt P28005 · UniProt P53218 · UniProt P38291 · UniProt P38208 · UniProt P38786 · UniProt P40571
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