Research workbench
Crystal structure of the hutp antitermination complex bound to the hut mRNA
Analyse Crystal structure of the hutp antitermination complex bound to the hut mRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BOY
- Type
- protein + RNA
- Length
- 462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP *GP*UP*UP*U)-3'; Hut operon…
- UniProt
- P10943
- Ligands
- HIS, MG
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-R(*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP *GP*UP*UP*U)-3' | rna | 21 | — | — |
| A, B, C | Hut operon positive regulatory protein | protein | 147 | 37% helix, 30% strand | P10943 |
Ligands and binding sites
- HIS · Histidine · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.70 | 0.96 | 21 | HIS |
| 2 | 72 | 0.70 | 0.95 | 19 | HIS |
| 3 | 108 | 0.63 | 0.88 | 30 | HIS |
| 4 | 165 | 0.49 | 0.77 | 30 | empty |
| 5 | 67 | 0.29 | 0.74 | 18 | empty |
Interfaces
6 interfaces between chains.
- D–B · 825 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–A · 822 Ų buried · 23 hydrogen bonds · protein-nucleic
- D–C · 806 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 577 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 575 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3BOY · Crystal structure of the HutP antitermination complex bound to the HUT mRNA · the same entry in another collection · chain B against B, TM-score 1.00
- P10943 · AlphaFold monomer V2.0 prediction for hut operon positive regulatory protein (P10943) · a predicted model of the same protein · chain A against A, 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 P10943
- Elsewhere: RCSB PDB 3BOY · PDBe 3BOY · UniProt P10943
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