Research workbench
Structure of the GTPase heterodimer of human SRP54 and SRalpha
Analyse Structure of the GTPase heterodimer of human SRP54 and SRalpha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L3Q
- Type
- protein
- Length
- 1,144 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Homo sapiens
- Molecule
- Signal recognition particle 54 kDa protein; Signal recognition particle receptor subunit…
- UniProt
- P61011, P08240
- Ligands
- GNP, AMP, MG, SO4
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · resolution 3.2 · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Signal recognition particle 54 kDa protein | protein | 265 | 48% helix, 16% strand | P61011 |
| B, D | Signal recognition particle receptor subunit alpha | protein | 307 | 51% helix, 14% strand | P08240 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.81 | 0.87 | 75 | SO4, GNP, MG, AMP, GOL |
| 2 | 596 | 0.81 | 0.86 | 75 | SO4, GNP, MG, AMP, GOL |
| 3 | 721 | 0.71 | 0.78 | 43 | empty |
| 4 | 160 | 0.50 | 0.78 | 23 | empty |
| 5 | 92 | 0.45 | 0.80 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1702 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1664 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 754 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5L3Q · Structure of the GTPase heterodimer of human SRP54 and sralpha · the same entry in another collection · chain A against A, TM-score 1.00
- P08240 · AlphaFold monomer V2.0 prediction for signal recognition particle receptor subunit alpha… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P61011 · AlphaFold monomer V2.0 prediction for signal recognition particle 54 kda protein (P61011) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P61011
- Every structure of UniProt P08240
- Elsewhere: RCSB PDB 5L3Q · PDBe 5L3Q · UniProt P61011 · UniProt P08240
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