Research workbench
Crystal structure of E. COLI hfq in complex with AU6A RNA and ADP
Analyse Crystal structure of E. COLI hfq in complex with AU6A RNA and ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RER
- Type
- protein + RNA
- Length
- 375 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein hfq; 5'-R(*AP*UP*UP*UP*UP*UP*UP*A)-3'
- UniProt
- C5W5L7
- Ligands
- ADP, MG
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Protein hfq | protein | 60 | 23% helix, 50% strand | C5W5L7 |
| B | Protein hfq | protein | 62 | 23% helix, 48% strand | C5W5L7 |
| C | Protein hfq | protein | 64 | 20% helix, 47% strand | C5W5L7 |
| F | Protein hfq | protein | 61 | 21% helix, 49% strand | C5W5L7 |
| K | 5'-R(*AP*UP*UP*UP*UP*UP*UP*A)-3' | rna | 8 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains B, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.78 | 0.85 | 30 | MG |
| 2 | 54 | 0.36 | 0.79 | 13 | empty |
Interfaces
12 interfaces between chains.
- C–D · 778 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 693 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 690 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 668 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 665 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3RER · Crystal structure of E. coli Hfq in complex with AU6A RNA and ADP · 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 C5W5L7
- Elsewhere: RCSB PDB 3RER · PDBe 3RER · UniProt C5W5L7
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