Research workbench
Crystal structure of listeria monocytogenes hfq in complex with U6 RNA
Analyse Crystal structure of listeria monocytogenes hfq in complex with U6 RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NL3
- Type
- protein + RNA
- Length
- 887 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein hfq; 5'-R(*UP*UP*UP*UP*UP*U)-3'
- UniProt
- B8DG33
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 20% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, J, G, K | Protein hfq | protein | 73 | 21% helix, 45% strand | B8DG33 |
| A, E | Protein hfq | protein | 72 | 21% helix, 44% strand | B8DG33 |
| B, H | Protein hfq | protein | 71 | 21% helix, 46% strand | B8DG33 |
| C, I, L | Protein hfq | protein | 74 | 19% helix, 45% strand | B8DG33 |
| F | Protein hfq | protein | 75 | 20% helix, 44% strand | B8DG33 |
| R, Z | 5'-R(*UP*UP*UP*UP*UP*U)-3' | rna | 6 | — | — |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.78 | 0.86 | 33 | empty |
| 2 | 459 | 0.77 | 0.86 | 31 | empty |
| 3 | 265 | 0.56 | 0.77 | 40 | empty |
| 4 | 359 | 0.56 | 0.75 | 44 | empty |
| 5 | 142 | 0.45 | 0.77 | 25 | empty |
Interfaces
36 interfaces between chains.
- D–A · 924 Ų buried · 19 hydrogen bonds · protein-protein
- D–H · 906 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 893 Ų buried · 18 hydrogen bonds · protein-protein
- B–J · 891 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 885 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4NL3 · Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA · the same entry in another collection · chain D against D, 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 B8DG33
- Elsewhere: RCSB PDB 4NL3 · PDBe 4NL3 · UniProt B8DG33
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.