Research workbench
Crystal structure of E COLI hfq in complex with ADP
Analyse Crystal structure of E COLI hfq in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RES
- Type
- protein
- Length
- 725 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein hfq
- UniProt
- C5W5L7
- Ligands
- ADP
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein hfq | protein | 62 | 21% helix, 48% strand | C5W5L7 |
| B, E, F, G, H, I, K, L | Protein hfq | protein | 60 | 22% helix, 50% strand | C5W5L7 |
| C, D, J | Protein hfq | protein | 61 | 23% helix, 49% strand | C5W5L7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains B, C, D, E, F, A, H, I, J, K, L, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.72 | 0.89 | 23 | empty |
| 2 | 907 | 0.70 | 0.75 | 57 | empty |
| 3 | 655 | 0.67 | 0.76 | 41 | empty |
| 4 | 185 | 0.45 | 0.74 | 25 | empty |
| 5 | 60 | 0.29 | 0.75 | 14 | empty |
Interfaces
15 interfaces between chains.
- C–D · 690 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 676 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 674 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 671 Ų buried · 8 hydrogen bonds · protein-protein
- I–J · 664 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3RES · Crystal structure of E coli Hfq in complex with 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 3RES · PDBe 3RES · UniProt C5W5L7
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