Research workbench
Structure of staphylococcus aureus hfq in complex with A7 RNA
Analyse Structure of staphylococcus aureus hfq in complex with A7 RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QSU
- Type
- protein + RNA
- Length
- 859 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA chaperone hfq; RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
- UniProt
- E5RBT2
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I, C, F | RNA chaperone hfq | protein | 60 | 23% helix, 53% strand | E5RBT2 |
| B, H, K, G, J, N, S | RNA chaperone hfq | protein | 61 | 25% helix, 52% strand | E5RBT2 |
| M, E | RNA chaperone hfq | protein | 61 | 25% helix, 51% strand | E5RBT2 |
| D | RNA chaperone hfq | protein | 62 | 24% helix, 52% strand | E5RBT2 |
| R, P | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 29 copies · chains A, H, B, I, K, M, C, E, D, F, G, J, N, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.70 | 0.74 | 64 | ZN |
| 2 | 910 | 0.69 | 0.74 | 65 | ZN |
| 3 | 246 | 0.53 | 0.76 | 25 | empty |
| 4 | 110 | 0.39 | 0.76 | 23 | empty |
| 5 | 65 | 0.39 | 0.79 | 15 | ZN |
Interfaces
22 interfaces between chains.
- I–K · 752 Ų buried · 11 hydrogen bonds · protein-protein
- B–M · 748 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 735 Ų buried · 12 hydrogen bonds · protein-protein
- G–J · 735 Ų buried · 13 hydrogen bonds · protein-protein
- D–J · 728 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3QSU · Structure of Staphylococcus aureus Hfq in complex with A7 RNA · the same entry in another collection · 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 E5RBT2
- Elsewhere: RCSB PDB 3QSU · PDBe 3QSU · UniProt E5RBT2
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