Research workbench
Crystal structure of the tRNA domain of tmrna from thermus thermophilus HB8
Analyse Crystal structure of the tRNA domain of tmrna from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CZJ
- Type
- protein + RNA
- Length
- 730 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ssra-binding protein; Tmrna (63-mer)
- UniProt
- Q8RR57
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Ssra-binding protein | protein | 122 | 16% helix, 29% strand | Q8RR57 |
| C | Ssra-binding protein | protein | 118 | 16% helix, 33% strand | Q8RR57 |
| G | Ssra-binding protein | protein | 120 | 16% helix, 30% strand | Q8RR57 |
| B, D, F, H | Tmrna (63-mer) | rna | 62 | — | — |
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.86 | 0.89 | 86 | empty |
| 2 | 1061 | 0.84 | 0.85 | 98 | empty |
| 3 | 94 | 0.78 | 0.98 | 20 | empty |
| 4 | 69 | 0.68 | 0.94 | 26 | empty |
| 5 | 385 | 0.67 | 0.81 | 23 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1319 Ų buried · 40 hydrogen bonds · protein-nucleic
- C–D · 1301 Ų buried · 49 hydrogen bonds · protein-nucleic
- G–H · 1257 Ų buried · 38 hydrogen bonds · protein-nucleic
- E–F · 1236 Ų buried · 41 hydrogen bonds · protein-nucleic
- A–D · 550 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 2CZJ · Crystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8 · the same entry in another collection · chain H against H, TM-score 1.00
- Q8RR57 · AlphaFold monomer V2.0 prediction for ssra-binding protein (Q8RR57) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q8RR57
- Elsewhere: RCSB PDB 2CZJ · PDBe 2CZJ · UniProt Q8RR57
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.