MolNFT v1 · #154105 · protein + RNA
Cryo-EM structure of archaeal ribonuclease P with mature tRNA
6K0B · Ribonuclease P protein component 2: “Cryo-EM structure of archaeal ribonuclease P with mature tRNA”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.82). MolNFT v1 #154105 on GenesisL1: 3D structure, binding…
- PDB
- 6K0B
- Type
- protein + RNA
- Length
- 2,058 residues
- Chains
- 14
- 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 0.82
Structure
electron microscopy · 7 distinct chains · 40% 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 | 39% helix, 24% strand | Q57917 |
| C, D | Ribonuclease P protein component 3 (EC 3.1.26.5) | protein | 231 | 45% helix, 15% strand | Q58539 |
| E, F | Ribonuclease P protein component 1 (EC 3.1.26.5) | protein | 95 | 11% helix, 39% strand | Q57903 |
| G, H | Ribonuclease P protein component 4 (EC 3.1.26.5) | protein | 120 | 46% helix, 17% strand | Q58372 |
| I, J | 50S ribosomal protein L7AE | protein | 116 | 51% helix, 14% strand | P54066 |
| U, V | TRNA | rna | 83 | — | — |
| 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 | 812 | 0.82 | 0.86 | 43 | empty |
| 2 | 749 | 0.82 | 0.86 | 40 | empty |
| 3 | 888 | 0.80 | 0.84 | 47 | empty |
| 4 | 682 | 0.80 | 0.85 | 60 | empty |
| 5 | 1012 | 0.80 | 0.82 | 55 | empty |
Interfaces
36 interfaces between chains.
- H–Y · 1875 Ų buried · 40 hydrogen bonds · protein-nucleic
- G–X · 1821 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–X · 1426 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–Y · 1423 Ų buried · 20 hydrogen bonds · protein-nucleic
- U–X · 1050 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Compared structures
- 6K0B · cryo-EM structure of archaeal Ribonuclease P with mature tRNA · 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 6K0B · PDBe 6K0B · UniProt Q57917 · UniProt Q58539 · UniProt Q57903 · UniProt Q58372 · UniProt P54066
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