MolNFT v1 · #61464 · protein
Structures and conformations in solution of the signal recognition particle receptor from the archaeon pyrococcus furiosus
3DMD: “Structures and conformations in solution of the signal recognition particle receptor from the archaeon…”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.72). MolNFT v1 #61464 on GenesisL1: 3D structure, binding…
- 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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