MolNFT v1 · #62534 · protein
1.9 ångström crystal structure of the active form of the C5A peptidase from streptococcus pyogenes (scpa)
3EIF: “1.9 ångström crystal structure of the active form of the C5A peptidase from streptococcus pyogenes (scpa)”. X-ray diffraction, 3 ligands (CA, NA, SO4), 10 pockets (best druggability 0.77). MolNFT v1 #62534 on GenesisL1: 3D…
- 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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