MolNFT v1 · #139120 · protein
The X-ray crystal structure of a tetr family transcription regulator rcda involved in the regulation of biofilm formation in escherichia COLI
5X5I · Hth-type transcriptional regulator rcda: “The X-ray crystal structure of a tetr family transcription regulator rcda involved in the regulation of…”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #139120 on…
- PDB
- 5X5I
- Type
- protein
- Length
- 1,376 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional regulator rcda
- UniProt
- P75811
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional regulator rcda | protein | 169 | 70% helix, 0% strand | P75811 |
| B | Hth-type transcriptional regulator rcda | protein | 173 | 76% helix, 0% strand | P75811 |
| C | Hth-type transcriptional regulator rcda | protein | 171 | 73% helix, 0% strand | P75811 |
| D | Hth-type transcriptional regulator rcda | protein | 173 | 76% helix, 0% strand | P75811 |
| E | Hth-type transcriptional regulator rcda | protein | 174 | 76% helix, 0% strand | P75811 |
| F | Hth-type transcriptional regulator rcda | protein | 171 | 78% helix, 0% strand | P75811 |
| G | Hth-type transcriptional regulator rcda | protein | 174 | 75% helix, 0% strand | P75811 |
| H | Hth-type transcriptional regulator rcda | protein | 171 | 72% helix, 0% strand | P75811 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.78 | 0.80 | 86 | empty |
| 2 | 203 | 0.72 | 0.88 | 27 | empty |
| 3 | 218 | 0.70 | 0.87 | 28 | empty |
| 4 | 760 | 0.70 | 0.76 | 63 | empty |
| 5 | 309 | 0.69 | 0.83 | 30 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1899 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 1892 Ų buried · 19 hydrogen bonds · protein-protein
- B–G · 1843 Ų buried · 16 hydrogen bonds · protein-protein
- D–H · 1744 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 504 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 5X5I · The X-ray crystal structure of a TetR family transcription regulator RcdA involved in the… · the same entry in another collection · chain H against H, TM-score 1.00
- P75811 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator rcda (P75811) · a predicted model of the same protein · chain F against A, TM-score 0.94
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 P75811
- Elsewhere: RCSB PDB 5X5I · PDBe 5X5I · UniProt P75811
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