Research workbench
Crystal structure of a bacterial signal peptidase apo-enzyme, implications for signal peptide binding and the ser-lys dyad mechanism.
Analyse Crystal structure of a bacterial signal peptidase apo-enzyme, implications for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KN9
- Type
- protein
- Length
- 904 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal peptidase I
- EC
- 3.4.21.89
- UniProt
- P00803
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Signal peptidase I (EC 3.4.21.89) | protein | 234 | 7% helix, 46% strand | P00803 |
| B | Signal peptidase I (EC 3.4.21.89) | protein | 222 | 6% helix, 45% strand | P00803 |
| D | Signal peptidase I (EC 3.4.21.89) | protein | 214 | 6% helix, 44% strand | P00803 |
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.69 | 0.83 | 46 | empty |
| 2 | 146 | 0.45 | 0.76 | 28 | empty |
| 3 | 117 | 0.43 | 0.77 | 24 | empty |
| 4 | 72 | 0.31 | 0.74 | 14 | empty |
| 5 | 70 | 0.30 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1001 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 435 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 128 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1KN9 · Crystal structure of a bacterial signal peptidase apo-enzyme, implications for signal… · the same entry in another collection · chain A against A, TM-score 1.00
- P00803 · AlphaFold monomer V2.0 prediction for signal peptidase I (P00803) · 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 P00803
- Elsewhere: RCSB PDB 1KN9 · PDBe 1KN9 · UniProt P00803
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