Research workbench
Structure of signal peptide peptidase a with C-termini bound in the active sites: insights into specificity, self-processing and regulation
Analyse Structure of signal peptide peptidase a with C-termini bound in the active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KWB
- Type
- protein
- Length
- 1,865 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal peptide peptidase sppa
- EC
- 3.4.21.-
- UniProt
- O34525
- Pockets
- 20 · best druggability 0.59
Structure
x-ray diffraction · 7 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal peptide peptidase sppa (EC 3.4.21.-) | protein | 237 | 41% helix, 27% strand | O34525 |
| B | Signal peptide peptidase sppa (EC 3.4.21.-) | protein | 233 | 41% helix, 26% strand | O34525 |
| C | Signal peptide peptidase sppa (EC 3.4.21.-) | protein | 237 | 42% helix, 27% strand | O34525 |
| D | Signal peptide peptidase sppa (EC 3.4.21.-) | protein | 228 | 43% helix, 25% strand | O34525 |
| E, G | Signal peptide peptidase sppa (EC 3.4.21.-) | protein | 232 | 40% helix, 26% strand | O34525 |
| F | Signal peptide peptidase sppa (EC 3.4.21.-) | protein | 234 | 41% helix, 27% strand | O34525 |
| H | Signal peptide peptidase sppa (EC 3.4.21.-) | protein | 232 | 42% helix, 26% strand | O34525 |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.59 | 0.80 | 28 | empty |
| 2 | 220 | 0.58 | 0.80 | 30 | empty |
| 3 | 245 | 0.57 | 0.79 | 29 | empty |
| 4 | 163 | 0.55 | 0.81 | 23 | empty |
| 5 | 201 | 0.52 | 0.77 | 28 | empty |
Interfaces
16 interfaces between chains.
- A–B · 2374 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 2299 Ų buried · 36 hydrogen bonds · protein-protein
- F–G · 2228 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 2215 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2201 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4KWB · Structure of signal peptide peptidase A with C-termini bound in the active sites… · the same entry in another collection · chain H against H, TM-score 1.00
- O34525 · AlphaFold monomer V2.0 prediction for putative signal peptide peptidase sppa (O34525) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 O34525
- Elsewhere: RCSB PDB 4KWB · PDBe 4KWB · UniProt O34525
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