Research workbench
Aminoacyl-tRNA synthetase ribozyme
Analyse Aminoacyl-tRNA synthetase ribozyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CUL
- Type
- protein + RNA
- Length
- 367 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
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | RNA (92-mer) | rna | 92 | — | — |
| D | RNA (92-mer) | rna | 92 | — | — |
| A | U1 small nuclear ribonucleoprotein a | protein | 92 | 30% helix, 22% strand | P09012 |
| B | U1 small nuclear ribonucleoprotein a | protein | 91 | 33% helix, 26% strand | P09012 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.66 | 0.74 | 42 | MG |
| 2 | 731 | 0.65 | 0.75 | 39 | MG, K |
| 3 | 396 | 0.61 | 0.78 | 28 | empty |
| 4 | 132 | 0.53 | 0.81 | 20 | empty |
| 5 | 125 | 0.51 | 0.81 | 18 | empty |
Interfaces
3 interfaces between chains.
- D–B · 907 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–A · 868 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–B · 411 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered, nucleotide modification).
Compared structures
- 3CUL · 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 3CUL · PDBe 3CUL · UniProt P09012
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