Research workbench
Crystal structure of a serine protease from streptococcus species
Analyse Crystal structure of a serine protease from streptococcus species in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XYA
- Type
- protein
- Length
- 1,358 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chemokine protease C
- UniProt
- Q3HV58
- Ligands
- AES, CA, SO4
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chemokine protease C | protein | 1358 | 10% helix, 33% strand | Q3HV58 |
Ligands and binding sites
- AES · 4-(2-aminoethyl)benzenesulfonyl fluoride · ligand · chains A
- CA · Calcium ion · metal · 4 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.75 | 0.78 | 96 | SO4 |
| 2 | 806 | 0.73 | 0.78 | 83 | empty |
| 3 | 59 | 0.72 | 0.98 | 22 | empty |
| 4 | 725 | 0.72 | 0.78 | 91 | empty |
| 5 | 272 | 0.69 | 0.84 | 26 | empty |
Modifications
Observed in the structure: 25 modified, 1 covalent (engineered, covalent ligand).
Compared structures
- 5XYA · Crystal structure of a serine protease from Streptococcus species · 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 5XYA · PDBe 5XYA · UniProt Q3HV58
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