MolNFT v1 · #125265 · protein
Structure of the crenarchaeal SRP54 GTPase bound to GDP
5L3V · Signal recognition particle 54 kda protein: “Structure of the crenarchaeal SRP54 GTPase bound to GDP”. X-ray diffraction, 2 ligands (GDP, SO4), 5 pockets (best druggability 0.66). MolNFT v1 #125265 on GenesisL1: 3D structure…
- PDB
- 5L3V
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle 54 kda protein
- UniProt
- Q97ZE7
- Ligands
- GDP, SO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle 54 kda protein | protein | 291 | 52% helix, 15% strand | Q97ZE7 |
| B | Signal recognition particle 54 kda protein | protein | 292 | 53% helix, 15% strand | Q97ZE7 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.66 | 0.76 | 51 | empty |
| 2 | 110 | 0.56 | 0.84 | 22 | empty |
| 3 | 185 | 0.52 | 0.78 | 42 | empty |
| 4 | 84 | 0.39 | 0.77 | 15 | empty |
| 5 | 89 | 0.31 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 620 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5L3V · Structure of the crenarchaeal SRP54 GTPase bound to GDP · 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 B against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 5L3V · PDBe 5L3V · UniProt Q97ZE7
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