Research workbench
The crystal structure of the signal recognition particle (srp) in complex with its RECEPTOR(SR)
Analyse The crystal structure of the signal recognition particle (srp) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XXA
- Type
- protein + RNA
- Length
- 1,592 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle protein; Srp receptor ftsy; 4.5S RNA
- EC
- 3.6.5.4
- UniProt
- P0AGD7, P10121
- Ligands
- GCP, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle protein (EC 3.6.5.4) | protein | 413 | 56% helix, 9% strand | P0AGD7 |
| B, D | Srp receptor ftsy | protein | 283 | 46% helix, 13% strand | P10121 |
| C | Signal recognition particle protein (EC 3.6.5.4) | protein | 409 | 55% helix, 10% strand | P0AGD7 |
| F, G | 4.5S RNA | rna | 102 | — | — |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.84 | 0.90 | 87 | GCP, MG |
| 2 | 466 | 0.84 | 0.92 | 78 | GCP, MG |
| 3 | 687 | 0.73 | 0.80 | 49 | empty |
| 4 | 637 | 0.73 | 0.81 | 41 | empty |
| 5 | 205 | 0.62 | 0.84 | 21 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1732 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1701 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 814 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–G · 790 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–G · 772 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 2XXA · The Crystal Structure of the Signal Recognition Particle (SRP) in Complex with its… · the same entry in another collection · chain G against G, TM-score 1.00
- P10121 · AlphaFold monomer V2.0 prediction for signal recognition particle receptor ftsy (P10121) · a predicted model of the same protein · chain B against A, TM-score 0.93
- P0AGD7 · AlphaFold monomer V2.0 prediction for signal recognition particle protein (P0AGD7) · a predicted model of the same protein · chain C against A, TM-score 0.66
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 P0AGD7
- Every structure of UniProt P10121
- Elsewhere: RCSB PDB 2XXA · PDBe 2XXA · UniProt P0AGD7 · UniProt P10121
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