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
- 6Y32
- Type
- protein
- Length
- 2,288 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle 54 kda protein; Signal recognition particle receptor subunit…
- UniProt
- P61011, P08240
- Ligands
- GNP, MG, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle 54 kda protein | protein | 274 | 48% helix, 15% strand | P61011 |
| B | Signal recognition particle receptor subunit alpha | protein | 302 | 52% helix, 14% strand | P08240 |
| C, E | Signal recognition particle 54 kda protein | protein | 268 | 49% helix, 16% strand | P61011 |
| D | Signal recognition particle receptor subunit alpha | protein | 305 | 53% helix, 13% strand | P08240 |
| F | Signal recognition particle receptor subunit alpha | protein | 304 | 52% helix, 14% strand | P08240 |
| G | Signal recognition particle 54 kda protein | protein | 267 | 49% helix, 16% strand | P61011 |
| H | Signal recognition particle receptor subunit alpha | protein | 300 | 53% helix, 13% strand | P08240 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 14 copies · chains B, D, C, F, G, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.87 | 0.88 | 127 | GNP, MG, SO4 |
| 2 | 498 | 0.83 | 0.89 | 70 | GNP, MG |
| 3 | 791 | 0.82 | 0.85 | 102 | GNP, MG, SO4 |
| 4 | 592 | 0.81 | 0.87 | 79 | GNP, MG |
| 5 | 360 | 0.57 | 0.75 | 44 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1653 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1644 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1609 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1603 Ų buried · 27 hydrogen bonds · protein-protein
- A–H · 618 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6Y32 · Structure of the GTPase heterodimer of human SRP54 and SRalpha · the same entry in another collection · chain H against H, 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 F against A, TM-score 0.97
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 6Y32 · PDBe 6Y32 · UniProt P61011 · UniProt P08240
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