Research workbench
Crystal structure of a serine protease from streptococcus pyogenes
Analyse Crystal structure of a serine protease from streptococcus pyogenes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EDD
- Type
- protein
- Length
- 1,394 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C5A peptidase
- EC
- 3.4.21.110
- UniProt
- Q3HV58
- Ligands
- CA, MG, SO4, CL
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C5A peptidase (EC 3.4.21.110) | protein | 1394 | 12% helix, 37% strand | Q3HV58 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A
- MG · Magnesium ion · metal
- SO4 · Sulfate ion · ion · 3 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.72 | 0.79 | 80 | SO4 |
| 2 | 62 | 0.72 | 0.98 | 23 | empty |
| 3 | 61 | 0.72 | 0.98 | 21 | empty |
| 4 | 251 | 0.68 | 0.85 | 27 | CA, GOL |
| 5 | 693 | 0.67 | 0.76 | 58 | empty |
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 7EDD · Crystal structure of a serine protease from Streptococcus pyogenes · 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 Q3HV58
- Elsewhere: RCSB PDB 7EDD · PDBe 7EDD · UniProt Q3HV58
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