Research workbench
1.9 ångström crystal structure of the active form of the C5A peptidase from streptococcus pyogenes (scpa)
Analyse 1.9 ångström crystal structure of the active form of the C5A peptidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EIF
- Type
- protein
- Length
- 936 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C5A peptidase
- EC
- 3.4.21.110
- UniProt
- B6ETQ5
- Ligands
- CA, NA, SO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C5A peptidase (EC 3.4.21.110) | protein | 936 | 18% helix, 34% strand | B6ETQ5 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
- MLA · Malonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.77 | 0.80 | 109 | SO4, EPE |
| 2 | 74 | 0.70 | 0.96 | 26 | empty |
| 3 | 74 | 0.54 | 0.86 | 22 | empty |
| 4 | 221 | 0.52 | 0.77 | 22 | empty |
| 5 | 121 | 0.43 | 0.77 | 25 | empty |
Compared structures
- 3EIF · 1.9 angstrom crystal structure of the active form of the C5a peptidase from Streptococcus… · 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 B6ETQ5
- Elsewhere: RCSB PDB 3EIF · PDBe 3EIF · UniProt B6ETQ5
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