MolNFT v1 · #105126 · protein + RNA
E.COLI hfq in complex with RNA ads
4QVD · RNA-binding protein hfq: “E.COLI hfq in complex with RNA ads”. X-ray diffraction, 2 pockets (best druggability 0.70). MolNFT v1 #105126 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QVD
- Type
- protein + RNA
- Length
- 367 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-binding protein hfq; RNA (5'-R(*AP*AP*CP*UP*AP*AP*A)-3')
- UniProt
- C1IFD2
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | RNA-binding protein hfq | protein | 60 | 23% helix, 50% strand | C1IFD2 |
| C | RNA-binding protein hfq | protein | 62 | 21% helix, 48% strand | C1IFD2 |
| F | RNA-binding protein hfq | protein | 61 | 23% helix, 51% strand | C1IFD2 |
| H | RNA (5'-R(*AP*AP*CP*UP*AP*AP*A)-3') | rna | 4 | — | — |
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 | 916 | 0.70 | 0.75 | 61 | empty |
| 2 | 61 | 0.28 | 0.73 | 19 | empty |
Interfaces
8 interfaces between chains.
- C–D · 714 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 709 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 669 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 668 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 667 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4QVD · E.coli Hfq in complex with RNA Ads · the same entry in another collection · chain H against H, 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 C1IFD2
- Elsewhere: RCSB PDB 4QVD · PDBe 4QVD · UniProt C1IFD2
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