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The crystal structure of the C-terminal domain of the two- component response regulator yesn from fusobacterium nucleatum subsp. nucleatum atcc 25586
Analyse The crystal structure of the C-terminal domain of the two- component response… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LSG
- Type
- protein
- Length
- 500 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Two-component response regulator yesn
- UniProt
- Q8RGT8
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Two-component response regulator yesn | protein | 103 | 72% helix, 0% strand | Q8RGT8 |
| C | Two-component response regulator yesn | protein | 102 | 73% helix, 0% strand | Q8RGT8 |
| D | Two-component response regulator yesn | protein | 95 | 73% helix, 0% strand | Q8RGT8 |
| E | Two-component response regulator yesn | protein | 97 | 72% helix, 0% strand | Q8RGT8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.83 | 0.90 | 40 | empty |
| 2 | 474 | 0.83 | 0.90 | 38 | PO4 |
| 3 | 548 | 0.71 | 0.80 | 43 | empty |
| 4 | 409 | 0.68 | 0.80 | 42 | empty |
| 5 | 77 | 0.40 | 0.79 | 21 | empty |
Interfaces
9 interfaces between chains.
- A–B · 799 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 794 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 546 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 394 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 218 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3LSG · The crystal structure of the C-terminal domain of the two-component response regulator… · 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 Q8RGT8
- Elsewhere: RCSB PDB 3LSG · PDBe 3LSG · UniProt Q8RGT8
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