Research workbench
Structures and conformations in solution of the signal recognition particle receptor from the archaeon pyrococcus furiosus
Analyse Structures and conformations in solution of 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
- 3DMD
- Type
- protein
- Length
- 948 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle receptor
- UniProt
- Q8U051
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Signal recognition particle receptor | protein | 320 | 54% helix, 15% strand | Q8U051 |
| A | Signal recognition particle receptor | protein | 310 | 53% helix, 15% strand | Q8U051 |
| C | Signal recognition particle receptor | protein | 318 | 54% helix, 15% strand | Q8U051 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains B, A, C
- GOL · Glycerol · additive · 6 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.72 | 0.85 | 41 | SO4 |
| 2 | 445 | 0.71 | 0.82 | 49 | empty |
| 3 | 349 | 0.66 | 0.81 | 43 | empty |
| 4 | 352 | 0.57 | 0.76 | 33 | empty |
| 5 | 129 | 0.52 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 526 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 372 Ų buried · 5 hydrogen bonds · protein-protein
- B–A · 304 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3DMD · Structures and Conformations in Solution of the Signal Recognition Particle Receptor from… · the same entry in another collection · chain B against B, TM-score 1.00
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 Q8U051
- Elsewhere: RCSB PDB 3DMD · PDBe 3DMD · UniProt Q8U051
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