MolNFT v1 · #77430 · protein + RNA
Crystal structure of E. COLI hfq in complex with AU6A RNA and ADP
3RER · Protein hfq: “Crystal structure of E. COLI hfq in complex with AU6A RNA and ADP”. X-ray diffraction, 2 ligands (ADP, MG), 2 pockets (best druggability 0.78). MolNFT v1 #77430 on GenesisL1: 3D structure, binding sites and pockets in…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.