Research workbench
Recognition of a signal peptide by the signal recognition particle
Analyse Recognition of a signal peptide by the signal recognition particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KL4
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition 54 kda protein; Signal peptide of yeast dipeptidyl aminopeptidase B
- EC
- 3.6.5.4, 3.4.14.-
- UniProt
- Q97ZE7, P18962
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition 54 kda protein (EC 3.6.5.4) | protein | 412 | 54% helix, 10% strand | Q97ZE7 |
| B | Signal peptide of yeast dipeptidyl aminopeptidase B (EC 3.4.14.-) | protein | 20 | 50% helix, 0% strand | P18962 |
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 | 803 | 0.74 | 0.79 | 72 | empty |
| 2 | 182 | 0.46 | 0.75 | 24 | empty |
| 3 | 59 | 0.41 | 0.81 | 16 | empty |
| 4 | 103 | 0.38 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 498 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3KL4 · Recognition of a signal peptide by the signal recognition particle · the same entry in another collection · chain A against A, TM-score 1.00
- Q97ZE7 · AlphaFold monomer V2.0 prediction for signal recognition particle 54 kda protein (Q97ZE7) · a predicted model of the same protein · chain A against A, TM-score 0.84
- P18962 · AlphaFold monomer V2.0 prediction for dipeptidyl aminopeptidase B (P18962) · a predicted model of the same protein · chain B against A, TM-score 0.28
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 Q97ZE7
- Every structure of UniProt P18962
- Elsewhere: RCSB PDB 3KL4 · PDBe 3KL4 · UniProt Q97ZE7 · UniProt P18962
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