MolNFT v1 · #109198 · protein
Crystal structure of the type-I signal peptidase from staphylococcus aureus (spsb) in complex with a substrate peptide (PEP2).
4WVI · Maltose-binding periplasmic PROTEIN,SIGNAL peptidase ib: “Crystal structure of the type-I signal peptidase from staphylococcus aureus (spsb) in complex with a…”. X-ray diffraction, 1 ligand (GLC), 4 pockets (best druggability 0.72).…
- PDB
- 4WVI
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,SIGNAL peptidase ib; Substrate peptide (PEP2)
- EC
- 3.4.21.89
- UniProt
- P0AEY0, Q5HHB9
- Ligands
- GLC
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic PROTEIN,SIGNAL peptidase ib (EC 3.4.21.89) | protein | 521 | 36% helix, 25% strand | P0AEY0, Q5HHB9 |
| D | Substrate peptide (PEP2) | protein | 11 | 0% helix, 27% strand | — |
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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.72 | 0.83 | 36 | GLC |
| 2 | 231 | 0.47 | 0.73 | 28 | empty |
| 3 | 60 | 0.37 | 0.79 | 20 | empty |
| 4 | 102 | 0.36 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–D · 595 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4WVI · Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in… · 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 4WVI · PDBe 4WVI · UniProt P0AEY0 · UniProt Q5HHB9
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