Research workbench
Crystal structure of flhf in complex with its activator
Analyse Crystal structure of flhf in complex with its activator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SYN
- Type
- protein
- Length
- 1,096 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flagellar biosynthesis protein flhf; ATP-binding protein ylxh
- UniProt
- Q01960, P40742
- Ligands
- GDP, AF3, MG, SO4
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Flagellar biosynthesis protein flhf | protein | 258 | 45% helix, 16% strand | Q01960 |
| E, F, G, H | ATP-binding protein ylxh | protein | 16 | 69% helix, 0% strand | P40742 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, E, F, C, D, G, H
- AF3 · Aluminum fluoride · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.84 | 0.92 | 61 | GDP, MG, AF3, SO4 |
| 2 | 424 | 0.82 | 0.91 | 67 | GDP, MG, AF3, SO4 |
| 3 | 128 | 0.79 | 0.97 | 35 | empty |
| 4 | 129 | 0.78 | 0.96 | 36 | empty |
| 5 | 450 | 0.62 | 0.77 | 40 | SO4 |
Interfaces
14 interfaces between chains.
- C–D · 1432 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1413 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 601 Ų buried · 4 hydrogen bonds · protein-protein
- C–G · 565 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 561 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3SYN · Crystal structure of FlhF in complex with its activator · the same entry in another collection · chain H against H, TM-score 1.00
- Q01960 · AlphaFold monomer V2.0 prediction for flagellar biosynthesis protein flhf (Q01960) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q01960
- Every structure of UniProt P40742
- Elsewhere: RCSB PDB 3SYN · PDBe 3SYN · UniProt Q01960 · UniProt P40742
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