Research workbench
Crystal structure of hfq from pseudomonas aeruginosa in complex with CTP
Analyse Crystal structure of hfq from pseudomonas aeruginosa in complex with CTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J6W
- Type
- protein
- Length
- 399 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein hfq
- UniProt
- Q9HUM0
- Ligands
- CTP, C, CDP, MG, NA, CL
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein hfq | protein | 67 | 19% helix, 43% strand | Q9HUM0 |
| B, C | Protein hfq | protein | 66 | 20% helix, 45% strand | Q9HUM0 |
| D | Protein hfq | protein | 65 | 20% helix, 45% strand | Q9HUM0 |
| E | Protein hfq | protein | 66 | 20% helix, 44% strand | Q9HUM0 |
| F | Protein hfq | protein | 69 | 19% helix, 43% strand | Q9HUM0 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 6 copies · chains A, E, B, D, C, F
- C · Cytidine-5'-monophosphate · ligand · 4 copies · chains A, E, C, F, B, D
- CDP · Cytidine-5'-diphosphate · ligand · chains C, D, F
- MG · Magnesium ion · metal · 8 copies · chains A, C, E, D
- NA · Sodium ion · metal · 3 copies · chains F
- CL · Chloride ion · ion · 2 copies · chains E, D, F
- P6G · Hexaethylene glycol · additive · chains A, B, C, D, E, F
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 | 919 | 0.72 | 0.76 | 59 | C, NA, CTP, MG, P6G, CDP |
Interfaces
6 interfaces between chains.
- D–F · 834 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 802 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 748 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 746 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 742 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4J6W · Crystal structure of HFQ from Pseudomonas aeruginosa in complex with CTP · 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 D against A, TM-score 0.99
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 4J6W · PDBe 4J6W · UniProt Q9HUM0
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