MolNFT v1 · #136156 · protein + DNA
Escherichia COLI hfq bound to dsdna
5UK7 · RNA-binding protein hfq: “Escherichia COLI hfq bound to dsdna”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.76). MolNFT v1 #136156 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UK7
- Type
- protein + DNA
- Length
- 872 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-binding protein hfq; DNA (5'- D(P*CP*GP*GP*CP*AP*AP*AP*AP*AP*AP*CP*GP*GP*CP*AP*AP*AP*A…
- UniProt
- A0A148HSM9
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-binding protein hfq | protein | 64 | 20% helix, 38% strand | A0A148HSM9 |
| B, C, D, G | RNA-binding protein hfq | protein | 67 | 19% helix, 46% strand | A0A148HSM9 |
| E, L | RNA-binding protein hfq | protein | 66 | 20% helix, 44% strand | A0A148HSM9 |
| F, J | RNA-binding protein hfq | protein | 65 | 18% helix, 46% strand | A0A148HSM9 |
| H, I | RNA-binding protein hfq | protein | 65 | 20% helix, 46% strand | A0A148HSM9 |
| K | RNA-binding protein hfq | protein | 68 | 18% helix, 41% strand | A0A148HSM9 |
| N, Z | DNA (5'- D(P*CP*GP*GP*CP*AP*AP*AP*AP*AP*AP*CP*GP*GP*CP*AP*AP*AP*AP*AP*A)-3') | dna | 20 | — | — |
| M, Y | DNA (5'- D(P*TP*TP*TP*TP*TP*TP*GP*CP*CP*GP*TP*TP*TP*TP*TP*TP*GP*CP*CP*G)-3') | dna | 20 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.76 | 0.80 | 63 | ZN |
| 2 | 1053 | 0.73 | 0.76 | 66 | ZN |
| 3 | 443 | 0.61 | 0.76 | 28 | empty |
| 4 | 289 | 0.55 | 0.76 | 30 | empty |
| 5 | 334 | 0.52 | 0.73 | 37 | empty |
Interfaces
26 interfaces between chains.
- B–C · 869 Ų buried · 12 hydrogen bonds · protein-protein
- N–M · 868 Ų buried · 95 hydrogen bonds · nucleic-nucleic
- F–J · 850 Ų buried · 13 hydrogen bonds · protein-protein
- Y–Z · 849 Ų buried · 95 hydrogen bonds · nucleic-nucleic
- D–E · 840 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5UK7 · Escherichia coli Hfq bound to dsDNA · 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 A0A148HSM9
- Elsewhere: RCSB PDB 5UK7 · PDBe 5UK7 · UniProt A0A148HSM9
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