MolNFT v1 · #60534 · protein + RNA
Aminoacyl-tRNA synthetase ribozyme
3CUN · RNA (92-mer): “Aminoacyl-tRNA synthetase ribozyme”. X-ray diffraction, 3 ligands (MG, K, CO), 8 pockets (best druggability 0.69). MolNFT v1 #60534 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3CUN
- Type
- protein + RNA
- Length
- 366 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (92-mer); U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- MG, K, CO
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | RNA (92-mer) | rna | 92 | — | — |
| A | U1 small nuclear ribonucleoprotein a | protein | 91 | 34% helix, 22% strand | P09012 |
| B | U1 small nuclear ribonucleoprotein a | protein | 91 | 30% helix, 26% strand | P09012 |
Ligands and binding sites
- MG · Magnesium ion · metal · 9 copies · chains C, D
- K · Potassium ion · metal · chains C
- CO · Cobalt (II) ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.69 | 0.75 | 48 | MG, K |
| 2 | 599 | 0.67 | 0.78 | 49 | empty |
| 3 | 877 | 0.66 | 0.74 | 39 | MG |
| 4 | 376 | 0.56 | 0.76 | 31 | empty |
| 5 | 120 | 0.54 | 0.82 | 19 | empty |
Interfaces
3 interfaces between chains.
- D–B · 954 Ų buried · 32 hydrogen bonds · protein-nucleic
- C–A · 863 Ų buried · 35 hydrogen bonds · protein-nucleic
- A–B · 412 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered, nucleotide modification).
Compared structures
- 3CUN · Aminoacyl-tRNA synthetase ribozyme · the same entry in another collection · chain C against C, 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 P09012
- Elsewhere: RCSB PDB 3CUN · PDBe 3CUN · UniProt P09012
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