MolNFT v1 · #177663 · protein
Crystal structure of signal recognition particle 54 kda protein (SRP54) from aeropyrum pernix K1 in complex with GDP
7EPK: “Crystal structure of signal recognition particle 54 kda protein (SRP54) from aeropyrum pernix K1 in complex…”. X-ray diffraction, 2 ligands (GDP, MG), 4 pockets (best druggability 0.62). MolNFT v1 #177663 on GenesisL1: 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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