Research workbench
Cryo-EM structure of an archaeal ribonuclease P
Analyse Cryo-EM structure of an archaeal ribonuclease P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K0A
- Type
- protein + RNA
- Length
- 1,880 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease P protein component 2; Ribonuclease P protein component 3; Ribonuclease P…
- EC
- 3.1.26.5
- UniProt
- Q57917, Q58539, Q57903, Q58372, P54066
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 6 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease P protein component 2 (EC 3.1.26.5) | protein | 126 | 34% helix, 22% strand | Q57917 |
| C, D | Ribonuclease P protein component 3 (EC 3.1.26.5) | protein | 226 | 46% helix, 17% strand | Q58539 |
| E, F | Ribonuclease P protein component 1 (EC 3.1.26.5) | protein | 95 | 4% helix, 39% strand | Q57903 |
| G, H | Ribonuclease P protein component 4 (EC 3.1.26.5) | protein | 119 | 50% helix, 15% strand | Q58372 |
| I, J | 50S ribosomal protein L7AE | protein | 116 | 50% helix, 14% strand | P54066 |
| X, Y | Rpr | rna | 258 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains G, H
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 | 1078 | 0.78 | 0.81 | 53 | empty |
| 2 | 1009 | 0.78 | 0.81 | 39 | empty |
| 3 | 676 | 0.78 | 0.84 | 41 | empty |
| 4 | 1192 | 0.78 | 0.81 | 56 | empty |
| 5 | 963 | 0.77 | 0.80 | 66 | empty |
Interfaces
24 interfaces between chains.
- G–X · 1769 Ų buried · 34 hydrogen bonds · protein-nucleic
- H–Y · 1665 Ų buried · 34 hydrogen bonds · protein-nucleic
- A–X · 1193 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–Y · 1080 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–D · 857 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6K0A · cryo-EM structure of an archaeal Ribonuclease P · the same entry in another collection · chain Y against Y, 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 Q57917
- Every structure of UniProt Q58539
- Every structure of UniProt Q57903
- Every structure of UniProt Q58372
- Every structure of UniProt P54066
- Elsewhere: RCSB PDB 6K0A · PDBe 6K0A · UniProt Q57917 · UniProt Q58539 · UniProt Q57903 · UniProt Q58372 · UniProt P54066
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