Research workbench
Crystal structure of ymah (hfq) from bacillus subtilis in complex with an RNA aptamer
Analyse Crystal structure of ymah (hfq) from bacillus subtilis in complex with an RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HSB
- Type
- protein + RNA
- Length
- 411 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein hfq; RNA (5'-R(*AP*GP*AP*GP*AP*GP*A)-3')
- UniProt
- O31796
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Protein hfq | protein | 67 | 21% helix, 48% strand | O31796 |
| B | Protein hfq | protein | 69 | 20% helix, 46% strand | O31796 |
| C | Protein hfq | protein | 66 | 21% helix, 47% strand | O31796 |
| E | Protein hfq | protein | 68 | 21% helix, 47% strand | O31796 |
| X | RNA (5'-R(*AP*GP*AP*GP*AP*GP*A)-3') | rna | 7 | — | — |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.69 | 0.75 | 52 | empty |
Interfaces
11 interfaces between chains.
- A–B · 831 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 825 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 803 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 793 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 772 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3HSB · Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer · the same entry in another collection · chain X against X, TM-score 1.00
- O31796 · AlphaFold monomer V2.0 prediction for RNA-binding protein hfq (O31796) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O31796
- Elsewhere: RCSB PDB 3HSB · PDBe 3HSB · UniProt O31796
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