Research workbench
Crystal structure of SPY0129, a streptococcus pyogenes class B sortase involved in pilus biogenesis
Analyse Crystal structure of SPY0129, a streptococcus pyogenes class B sortase involved… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PSQ
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical exported protein
- UniProt
- Q9A1S1
- Ligands
- ZN, CL
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical exported protein | protein | 186 | 23% helix, 32% strand | Q9A1S1 |
| B | Hypothetical exported protein | protein | 182 | 18% helix, 33% strand | Q9A1S1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 19 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- ACY · Acetic acid · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.67 | 0.82 | 36 | ACY |
| 2 | 87 | 0.44 | 0.80 | 19 | EDO |
| 3 | 142 | 0.43 | 0.76 | 26 | EDO, ZN |
Interfaces
1 interface between chains.
- A–B · 491 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3PSQ · Crystal structure of Spy0129, a Streptococcus pyogenes class B sortase involved in pilus… · 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 Q9A1S1
- Elsewhere: RCSB PDB 3PSQ · PDBe 3PSQ · UniProt Q9A1S1
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