MolNFT v1 · #129053 · protein
Conformational dynamism for DNA interaction in salmonella typhimurium rcsb response regulator.
5O8Y · Transcriptional regulatory protein rcsb: “Conformational dynamism for DNA interaction in salmonella typhimurium rcsb response regulator.”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.75). MolNFT v1 #129053 on…
- PDB
- 5O8Y
- Type
- protein
- Length
- 1,241 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulatory protein rcsb
- UniProt
- P58663
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Transcriptional regulatory protein rcsb | protein | 206 | 49% helix, 15% strand | P58663 |
| C, G, F | Transcriptional regulatory protein rcsb | protein | 207 | 51% helix, 15% strand | P58663 |
| H | Transcriptional regulatory protein rcsb | protein | 208 | 51% helix, 15% strand | P58663 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, C, D, G, F, H
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains A, D, G, C, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.75 | 0.86 | 24 | PE4 |
| 2 | 318 | 0.74 | 0.86 | 23 | PE4 |
| 3 | 725 | 0.66 | 0.75 | 76 | empty |
| 4 | 463 | 0.61 | 0.75 | 36 | empty |
| 5 | 485 | 0.60 | 0.74 | 42 | empty |
Interfaces
11 interfaces between chains.
- G–H · 1723 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1685 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 1641 Ų buried · 23 hydrogen bonds · protein-protein
- A–G · 458 Ų buried · 9 hydrogen bonds · protein-protein
- F–H · 411 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5O8Y · Conformational dynamism for DNA interaction in Salmonella typhimurium RcsB response… · the same entry in another collection · chain H against H, TM-score 1.00
- P58663 · AlphaFold monomer V2.0 prediction for transcriptional regulatory protein rcsb (P58663) · a predicted model of the same protein · chain H against A, TM-score 0.71
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 P58663
- Elsewhere: RCSB PDB 5O8Y · PDBe 5O8Y · UniProt P58663
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