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Crystal structure of pilf type IV pilus assembly ATPase from thermus thermophilus
Analyse Crystal structure of pilf type IV pilus assembly ATPase from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OIU
- Type
- protein
- Length
- 2,314 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type IV pilus assembly protein pilf
- UniProt
- Q5SLC9
- Ligands
- ATP, MG, ZN, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type IV pilus assembly protein pilf | protein | 385 | 37% helix, 29% strand | Q5SLC9 |
| B | Type IV pilus assembly protein pilf | protein | 385 | 38% helix, 30% strand | Q5SLC9 |
| C, D, E, F | Type IV pilus assembly protein pilf | protein | 386 | 38% helix, 28% strand | Q5SLC9 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 12 copies · chains A, F, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.84 | 0.85 | 104 | ATP, MG, CL |
| 2 | 1047 | 0.84 | 0.85 | 107 | ATP, MG, CL |
| 3 | 919 | 0.83 | 0.85 | 90 | ATP, MG, CL |
| 4 | 827 | 0.82 | 0.85 | 79 | ATP, MG, CL |
| 5 | 755 | 0.80 | 0.84 | 82 | ATP, MG, CL |
Interfaces
6 interfaces between chains.
- B–C · 1711 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1664 Ų buried · 31 hydrogen bonds · protein-protein
- B–E · 1622 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 1545 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 1539 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5OIU · Crystal structure of PilF type IV pilus assembly ATPase from Thermus thermophilus · the same entry in another collection · chain F against F, TM-score 1.00
- Q5SLC9 · AlphaFold monomer V2.0 prediction for type IV pilus assembly ATPase pilb (Q5SLC9) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q5SLC9
- Elsewhere: RCSB PDB 5OIU · PDBe 5OIU · UniProt Q5SLC9
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