Research workbench
Crystal structure of signal recognition particle 54 kda protein (SRP54) from aeropyrum pernix K1 in complex with GDP
Analyse Crystal structure of signal recognition particle 54 kda protein (SRP54) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EPK
- Type
- protein
- Length
- 426 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle 54 kda protein
- UniProt
- Q9YB62
- Ligands
- GDP, MG
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle 54 kda protein | protein | 426 | 56% helix, 10% strand | Q9YB62 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 273 | 0.62 | 0.80 | 45 | empty |
| 2 | 55 | 0.43 | 0.84 | 19 | MG |
| 3 | 80 | 0.38 | 0.77 | 17 | empty |
| 4 | 72 | 0.34 | 0.75 | 17 | empty |
Compared structures
- 7EPK · Crystal Structure of Signal Recognition Particle 54 kDa protein (SRP54) from Aeropyrum… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9YB62 · AlphaFold monomer V2.0 prediction for signal recognition particle 54 kda protein (Q9YB62) · a predicted model of the same protein · chain A against A, TM-score 0.74
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 Q9YB62
- Elsewhere: RCSB PDB 7EPK · PDBe 7EPK · UniProt Q9YB62
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