Research workbench
Structure of the Rap conjugation gene regulator of the plasmid pLS20 in complex with the Phr* peptide
Analyse Structure of the Rap conjugation gene regulator of the plasmid pLS20 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T46
- Type
- protein
- Length
- 1,468 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.45
- Source
- Bacillus subtilis subsp. natto; SYNTHETIC CONSTRUCT
- Molecule
- Response regulator aspartate phosphatase; Quorum-sensing secretion protein (processed)
- UniProt
- E9RIY6, E9RIY7
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.45 · 5 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Response regulator aspartate phosphatase | protein | 359 | 80% helix, 0% strand | E9RIY6 |
| B, D, F, H | Quorum-sensing secretion protein (processed) | protein | 5 | 0% helix, 0% strand | E9RIY7 |
| C | Response regulator aspartate phosphatase | protein | 363 | 81% helix, 1% strand | E9RIY6 |
| E | Response regulator aspartate phosphatase | protein | 361 | 79% helix, 0% strand | E9RIY6 |
| G | Response regulator aspartate phosphatase | protein | 365 | 79% helix, 0% strand | E9RIY6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.82 | 0.88 | 60 | empty |
| 2 | 397 | 0.75 | 0.85 | 49 | empty |
| 3 | 410 | 0.74 | 0.84 | 48 | empty |
| 4 | 757 | 0.71 | 0.77 | 54 | empty |
| 5 | 469 | 0.69 | 0.80 | 35 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1708 Ų buried · 24 hydrogen bonds · protein-protein
- E–G · 1498 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 696 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 684 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 683 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6T46 · Structure of the rap conjugation gene regulator of the plasmid PLS20 in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
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 E9RIY6
- Every structure of UniProt E9RIY7
- Elsewhere: RCSB PDB 6T46 · PDBe 6T46 · UniProt E9RIY6 · UniProt E9RIY7
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