Research workbench
Structural basis of signal sequence surveillance and selection by the srp-sr complex
Analyse Structural basis of signal sequence surveillance and selection by the srp-sr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZN8
- Type
- protein + RNA
- Length
- 790 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle protein; Signal recognition particle receptor ftsy; 4.5 S…
- EC
- 3.6.5.4, 3.4.14.-
- UniProt
- O07347, P10121, Q97ZE7, P18962
- Ligands
- MG
- Pockets
- 10 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle protein (EC 3.6.5.4) | protein | 287 | 48% helix, 11% strand | O07347 |
| D | Signal recognition particle receptor ftsy (EC 3.6.5.4) | protein | 295 | 40% helix, 12% strand | P10121 |
| G | 4.5 S RNA (EC 3.6.5.4) | rna | 88 | — | — |
| M | Signal recognition particle 54 kda protein (EC 3.6.5.4) | protein | 106 | 52% helix, 0% strand | Q97ZE7 |
| S | Dipeptidyl aminopeptidase B (EC 3.4.14.-) | protein | 14 | 43% helix, 0% strand | P18962 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.78 | 0.82 | 69 | empty |
| 2 | 1087 | 0.74 | 0.78 | 71 | empty |
| 3 | 338 | 0.55 | 0.75 | 25 | empty |
| 4 | 115 | 0.47 | 0.79 | 15 | empty |
| 5 | 70 | 0.44 | 0.82 | 17 | empty |
Interfaces
6 interfaces between chains.
- G–M · 792 Ų buried · 27 hydrogen bonds · protein-nucleic
- M–S · 622 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 582 Ų buried · 6 hydrogen bonds · protein-protein
- D–G · 385 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–M · 217 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3ZN8 · Structural Basis of Signal Sequence Surveillance and Selection by the SRP-SR Complex · the same entry in another collection · chain S against S, TM-score 1.00
- O07347 · AlphaFold monomer V2.0 prediction for signal recognition particle protein (O07347) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P10121 · AlphaFold monomer V2.0 prediction for signal recognition particle receptor ftsy (P10121) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q97ZE7 · AlphaFold monomer V2.0 prediction for signal recognition particle 54 kda protein (Q97ZE7) · a predicted model of the same protein · chain M against A, TM-score 0.69
- P18962 · AlphaFold monomer V2.0 prediction for dipeptidyl aminopeptidase B (P18962) · a predicted model of the same protein · chain S against A, TM-score 0.31
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 O07347
- Every structure of UniProt P10121
- Every structure of UniProt Q97ZE7
- Every structure of UniProt P18962
- Elsewhere: RCSB PDB 3ZN8 · PDBe 3ZN8 · UniProt O07347 · UniProt P10121 · UniProt Q97ZE7 · UniProt P18962
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