Research workbench
Crystal structure of hfq from pseudomonas aeruginosa in complex with ATP
Analyse Crystal structure of hfq from pseudomonas aeruginosa in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J5Y
- Type
- protein
- Length
- 409 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein hfq
- UniProt
- Q9HUM0
- Ligands
- ATP, NA
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Protein hfq | protein | 68 | 19% helix, 44% strand | Q9HUM0 |
| D | Protein hfq | protein | 68 | 19% helix, 44% strand | Q9HUM0 |
| F | Protein hfq | protein | 69 | 19% helix, 45% strand | Q9HUM0 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains A, F, B, C, D, E
- NA · Sodium ion · metal · 2 copies · chains A, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 931 | 0.71 | 0.75 | 60 | empty |
Interfaces
6 interfaces between chains.
- E–F · 856 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 846 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 834 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 778 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 744 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4J5Y · Crystal structure of Hfq from Pseudomonas aeruginosa in complex with ATP · the same entry in another collection · chain F against F, TM-score 1.00
- Q9HUM0 · AlphaFold monomer V2.0 prediction for RNA-binding protein hfq (Q9HUM0) · a predicted model of the same protein · chain F 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 Q9HUM0
- Elsewhere: RCSB PDB 4J5Y · PDBe 4J5Y · UniProt Q9HUM0
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