MolNFT v1 · #66506 · protein + RNA
Crystal structure of ymah (hfq) from bacillus subtilis in complex with an RNA aptamer
3HSB · Protein hfq: “Crystal structure of ymah (hfq) from bacillus subtilis in complex with an RNA aptamer”. X-ray diffraction, 1 pocket (best druggability 0.69). MolNFT v1 #66506 on GenesisL1: 3D structure, binding sites and pockets in…
- 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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