Research workbench
Crystal structure of the type-I signal peptidase from staphylococcus aureus (spsb).
Analyse Crystal structure of the type-I signal peptidase from staphylococcus aureus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WVG
- Type
- protein
- Length
- 513 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,SIGNAL peptidase ib
- EC
- 3.4.21.89
- UniProt
- P0AEY0, Q5HHB9
- Ligands
- GLC
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic PROTEIN,SIGNAL peptidase ib (EC 3.4.21.89) | protein | 513 | 36% helix, 26% strand | P0AEY0, Q5HHB9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
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 | 567 | 0.71 | 0.79 | 66 | GLC |
| 2 | 52 | 0.34 | 0.78 | 13 | empty |
| 3 | 80 | 0.31 | 0.73 | 17 | empty |
Compared structures
- 4WVG · Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB). · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HHB9 · AlphaFold monomer V2.0 prediction for signal peptidase ib (Q5HHB9) · a predicted model of the same protein · chain A against A, TM-score 0.31
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 P0AEY0
- Every structure of UniProt Q5HHB9
- Elsewhere: RCSB PDB 4WVG · PDBe 4WVG · UniProt P0AEY0 · UniProt Q5HHB9
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