MolNFT v1 · #33924 · protein + RNA
Crystal structure of the tRNA domain of tmrna from thermus thermophilus HB8
2CZJ · Ssra-binding protein: “Crystal structure of the tRNA domain of tmrna from thermus thermophilus HB8”. X-ray diffraction, 18 pockets (best druggability 0.86). MolNFT v1 #33924 on GenesisL1: 3D structure, binding sites and pockets in…
- 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
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