MolNFT v1 · #72595 · protein + RNA
Crystal structure of a signal sequence bound to the signal recognition particle
3NDB · Signal recognition particle 19 kda protein: “Crystal structure of a signal sequence bound to the signal recognition particle”. X-ray diffraction, 1 ligand (PO4), 12 pockets (best druggability 0.75). MolNFT v1 #72595 on GenesisL1: 3D…
- PDB
- 3NDB
- Type
- protein + RNA
- Length
- 643 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle 19 kda protein; Signal recognition 54 kda protein; Srp RNA
- UniProt
- Q58440, Q57565
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle 19 kda protein | protein | 87 | 38% helix, 10% strand | Q58440 |
| B | Signal recognition 54 kda protein | protein | 420 | 55% helix, 9% strand | Q57565 |
| M | Srp RNA | rna | 136 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains B
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 | 544 | 0.75 | 0.83 | 38 | empty |
| 2 | 311 | 0.71 | 0.85 | 27 | empty |
| 3 | 519 | 0.65 | 0.77 | 46 | empty |
| 4 | 288 | 0.64 | 0.80 | 30 | empty |
| 5 | 473 | 0.58 | 0.74 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–M · 1244 Ų buried · 34 hydrogen bonds · protein-nucleic
- B–M · 893 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 103 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3NDB · Crystal structure of a signal sequence bound to the signal recognition particle · the same entry in another collection · chain A against A, 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 0.96
- Q57565 · AlphaFold monomer V2.0 prediction for signal recognition particle 54 kda protein (Q57565) · a predicted model of the same protein · chain B 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 Q58440
- Every structure of UniProt Q57565
- Elsewhere: RCSB PDB 3NDB · PDBe 3NDB · UniProt Q58440 · UniProt Q57565
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