Research workbench
Crystal structure of pseudomonas aeruginosa PILY1 C-terminal domain
Analyse Crystal structure of pseudomonas aeruginosa PILY1 C-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HX6
- Type
- protein
- Length
- 977 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type 4 fimbrial biogenesis protein PILY1
- UniProt
- Q9HVM8
- Ligands
- CA
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type 4 fimbrial biogenesis protein PILY1 | protein | 491 | 11% helix, 38% strand | Q9HVM8 |
| B | Type 4 fimbrial biogenesis protein PILY1 | protein | 486 | 9% helix, 38% strand | Q9HVM8 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
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 | 934 | 0.79 | 0.81 | 106 | empty |
| 2 | 920 | 0.72 | 0.77 | 80 | empty |
| 3 | 185 | 0.70 | 0.88 | 28 | empty |
| 4 | 54 | 0.40 | 0.81 | 16 | empty |
| 5 | 86 | 0.39 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1038 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3HX6 · Crystal structure of Pseudomonas aeruginosa PilY1 C-terminal domain · the same entry in another collection · chain B against B, TM-score 1.00
- Q9HVM8 · AlphaFold monomer V2.0 prediction for type IV pilus biogenesis factor PILY1 (Q9HVM8) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9HVM8
- Elsewhere: RCSB PDB 3HX6 · PDBe 3HX6 · UniProt Q9HVM8
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