Research workbench
Atomic model of the srp-ftsy early conformation
Analyse Atomic model of the srp-ftsy early conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XKV
- Type
- protein + RNA
- Length
- 694 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle protein; 4.5S RNA; Cell division protein ftsy
- EC
- 3.6.5.4
- UniProt
- O07347, P0AGD7, P83749
- Pockets
- 8 · best druggability 0.74
Structure
electron microscopy · 4 distinct chains · 37% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle protein (EC 3.6.5.4) | protein | 290 | 38% helix, 14% strand | O07347 |
| B | 4.5S RNA | rna | 96 | — | — |
| C | Signal recognition particle protein | protein | 43 | 60% helix, 0% strand | P0AGD7 |
| D | Cell division protein ftsy | protein | 265 | 31% helix, 13% strand | P83749 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.74 | 0.78 | 62 | empty |
| 2 | 176 | 0.59 | 0.82 | 32 | empty |
| 3 | 112 | 0.57 | 0.84 | 27 | empty |
| 4 | 237 | 0.51 | 0.76 | 31 | empty |
| 5 | 228 | 0.48 | 0.74 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–D · 784 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 713 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–D · 194 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 2XKV · Atomic Model of the SRP-FtsY Early Conformation · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.96
- P83749 · AlphaFold monomer V2.0 prediction for signal recognition particle receptor ftsy (P83749) · a predicted model of the same protein · chain D against A, TM-score 0.94
- 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 0.91
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 P0AGD7
- Every structure of UniProt P83749
- Elsewhere: RCSB PDB 2XKV · PDBe 2XKV · UniProt O07347 · UniProt P0AGD7 · UniProt P83749
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