Research workbench
Crystal structure of type 1 signal peptidase from escherichia COLI in complex with a beta-lactam inhibitor
Analyse Crystal structure of type 1 signal peptidase from escherichia COLI in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B12
- Type
- protein
- Length
- 898 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
- Ligands
- 1PN, PO4
- Pockets
- 13 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal peptidase I (EC 3.4.21.89) | protein | 239 | 8% helix, 46% strand | P00803 |
| B | Signal peptidase I (EC 3.4.21.89) | protein | 211 | 6% helix, 44% strand | P00803 |
| C | Signal peptidase I (EC 3.4.21.89) | protein | 226 | 6% helix, 42% strand | P00803 |
| D | Signal peptidase I (EC 3.4.21.89) | protein | 222 | 6% helix, 47% strand | P00803 |
Ligands and binding sites
- 1PN · prop-2-en-1-yl (2S)-2-[(2S,3R)-3-(acetyloxy)-1-oxobutan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylate · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.65 | 0.77 | 57 | PO4 |
| 2 | 437 | 0.57 | 0.74 | 51 | empty |
| 3 | 147 | 0.49 | 0.78 | 27 | 1PN |
| 4 | 126 | 0.45 | 0.77 | 19 | 1PN |
| 5 | 220 | 0.45 | 0.73 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–D · 441 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 428 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 280 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 3 disulfide (covalent ligand, disulfide).
Compared structures
- 1B12 · Crystal structure of type 1 signal peptidase from escherichia COLI in complex with a… · the same entry in another collection · chain D against D, TM-score 1.00
- P00803 · AlphaFold monomer V2.0 prediction for signal peptidase I (P00803) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 1B12 · PDBe 1B12 · UniProt P00803
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