MolNFT v1 · #109774 · protein + RNA
Signal-sequence induced conformational changes in the signal recognition particle
4XCO · RNA: “Signal-sequence induced conformational changes in the signal recognition particle”. X-ray diffraction, 2 ligands (MG, NA), 12 pockets (best druggability 0.80). MolNFT v1 #109774 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4XCO
- Type
- protein + RNA
- Length
- 611 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA; Signal recognition particle 19 kda protein; Signal recognition particle 54 kda…
- UniProt
- Q58440, Q57565
- Ligands
- MG, NA
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M, E | RNA | rna | 96 | — | — |
| A | Signal recognition particle 19 kda protein | protein | 85 | 34% helix, 12% strand | Q58440 |
| B | Signal recognition particle 19 kda protein | protein | 84 | 31% helix, 12% strand | Q58440 |
| C | Signal recognition particle 54 kda PROTEIN,SIGNAL sequence | protein | 157 | 69% helix, 0% strand | Q57565 |
| D | Signal recognition particle 54 kda PROTEIN,SIGNAL sequence | protein | 93 | 72% helix, 0% strand | Q57565 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.80 | 0.82 | 79 | MG |
| 2 | 822 | 0.78 | 0.82 | 57 | MG |
| 3 | 342 | 0.70 | 0.84 | 26 | empty |
| 4 | 407 | 0.62 | 0.78 | 36 | empty |
| 5 | 437 | 0.60 | 0.77 | 25 | MG |
Interfaces
9 interfaces between chains.
- M–A · 1269 Ų buried · 36 hydrogen bonds · protein-nucleic
- E–B · 1257 Ų buried · 36 hydrogen bonds · protein-nucleic
- E–C · 630 Ų buried · 22 hydrogen bonds · protein-nucleic
- M–D · 589 Ų buried · 19 hydrogen bonds · protein-nucleic
- M–C · 284 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 4XCO · Signal-sequence induced conformational changes in the signal recognition particle · the same entry in another collection · chain B against B, TM-score 1.00
- Q58440 · AlphaFold monomer V2.0 prediction for signal recognition particle 19 kda protein (Q58440) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q57565 · AlphaFold monomer V2.0 prediction for signal recognition particle 54 kda protein (Q57565) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q58440
- Every structure of UniProt Q57565
- Elsewhere: RCSB PDB 4XCO · PDBe 4XCO · UniProt Q58440 · UniProt Q57565
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