Research workbench
Crystal structure xylellain, a cysteine protease from xylella fastidiosa
Analyse Crystal structure xylellain, a cysteine protease from xylella fastidiosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OIS
- Type
- protein
- Length
- 1,070 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine protease
- UniProt
- Q9PGZ0
- Ligands
- UDP
- Pockets
- 17 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cysteine protease | protein | 268 | 29% helix, 21% strand | Q9PGZ0 |
| B, C | Cysteine protease | protein | 267 | 28% helix, 21% strand | Q9PGZ0 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.65 | 0.79 | 48 | empty |
| 2 | 368 | 0.65 | 0.79 | 51 | empty |
| 3 | 441 | 0.63 | 0.77 | 45 | empty |
| 4 | 182 | 0.57 | 0.80 | 26 | UDP |
| 5 | 190 | 0.56 | 0.79 | 25 | UDP |
Interfaces
5 interfaces between chains.
- A–B · 2092 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2084 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 286 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 118 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3OIS · Crystal Structure Xylellain, a cysteine protease from Xylella fastidiosa · 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 Q9PGZ0
- Elsewhere: RCSB PDB 3OIS · PDBe 3OIS · UniProt Q9PGZ0
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