Research workbench
Crystal structure of escherichia COLI type I signal peptidase in complex with an arylomycin lipoglycopeptide antibiotic
Analyse Crystal structure of escherichia COLI type I signal peptidase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S04
- Type
- protein
- Length
- 444 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal peptidase I; Glyco-arylomycin
- EC
- 3.4.21.89
- UniProt
- P00803
- Ligands
- 02U, RAM
- Pockets
- 4 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal peptidase I (EC 3.4.21.89) | protein | 209 | 6% helix, 44% strand | P00803 |
| B | Signal peptidase I (EC 3.4.21.89) | protein | 223 | 6% helix, 46% strand | P00803 |
| I, J | Glyco-arylomycin | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- 02U · 14-methylhexadec-9-enoic acid · ligand · 2 copies · chains B, I, A, J
- RAM · alpha-L-rhamnopyranose · sugar · 2 copies · chains B, I, A, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.38 | 0.75 | 26 | empty |
| 2 | 104 | 0.36 | 0.75 | 27 | empty |
| 3 | 84 | 0.33 | 0.74 | 17 | empty |
| 4 | 51 | 0.28 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–J · 462 Ų buried · 10 hydrogen bonds · protein-protein
- B–I · 460 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 338 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent, 2 d-amino, 2 glycan, 1 disulfide (nonstandard, covalent ligand, D-amino acid, glycosylation, disulfide).
Compared structures
- 3S04 · Crystal structure of Escherichia coli type I signal peptidase in complex with an… · 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 A against A, TM-score 0.98
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 3S04 · PDBe 3S04 · UniProt P00803
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