Research workbench
Crystal structure of antitermination factors nusb and nuse in complex with dsrna
Analyse Crystal structure of antitermination factors nusb and nuse in complex with dsrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R2D
- Type
- protein + RNA
- Length
- 448 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N utilization substance protein B; 30S ribosomal protein S10…
- UniProt
- O66530, O66430
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 69% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N utilization substance protein B | protein | 132 | 81% helix, 0% strand | O66530 |
| B | N utilization substance protein B | protein | 138 | 79% helix, 0% strand | O66530 |
| J, K | 30S ribosomal protein S10 | protein | 79 | 33% helix, 43% strand | O66430 |
| R | 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3' | rna | 12 | — | — |
| S | 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3' | rna | 8 | — | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.72 | 0.78 | 56 | empty |
| 2 | 297 | 0.65 | 0.81 | 40 | empty |
| 3 | 357 | 0.62 | 0.79 | 31 | empty |
| 4 | 54 | 0.34 | 0.76 | 11 | empty |
| 5 | 52 | 0.32 | 0.76 | 12 | empty |
Interfaces
10 interfaces between chains.
- A–J · 856 Ų buried · 18 hydrogen bonds · protein-protein
- B–K · 852 Ų buried · 18 hydrogen bonds · protein-protein
- R–S · 391 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- B–S · 320 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–S · 293 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 3R2D · Crystal Structure of Antitermination Factors NusB and NusE in complex with dsRNA · the same entry in another collection · chain S against S, TM-score 1.00
- O66530 · AlphaFold monomer V2.0 prediction for transcription antitermination protein nusb (O66530) · a predicted model of the same protein · chain A against A, TM-score 0.98
- O66430 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S10 (O66430) · a predicted model of the same protein · chain J against A, TM-score 0.96
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 O66530
- Every structure of UniProt O66430
- Elsewhere: RCSB PDB 3R2D · PDBe 3R2D · UniProt O66530 · UniProt O66430
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