Research workbench
Fadr, fatty acid responsive transcription factor from vibrio cholerae, in complex with DNA
Analyse Fadr, fatty acid responsive transcription factor from vibrio cholerae, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P9U
- Type
- protein + DNA
- Length
- 1,212 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty acid metabolism regulator protein; DNA (31-mer)
- UniProt
- Q9KQU8
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, A, B | Fatty acid metabolism regulator protein | protein | 272 | 63% helix, 2% strand | Q9KQU8 |
| G, C | DNA (31-mer) | dna | 31 | — | — |
| H, D | DNA (31-mer) | dna | 31 | — | — |
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 | 772 | 0.76 | 0.81 | 78 | empty |
| 2 | 537 | 0.73 | 0.82 | 71 | empty |
| 3 | 152 | 0.59 | 0.83 | 26 | empty |
| 4 | 139 | 0.52 | 0.80 | 25 | empty |
| 5 | 295 | 0.51 | 0.74 | 38 | empty |
Interfaces
17 interfaces between chains.
- A–B · 1746 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1725 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1377 Ų buried · 141 hydrogen bonds · nucleic-nucleic
- C–D · 1371 Ų buried · 140 hydrogen bonds · nucleic-nucleic
- B–D · 512 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4P9U · FadR, Fatty Acid Responsive Transcription Factor from Vibrio cholerae, in Complex with DNA · the same entry in another collection · chain D against D, TM-score 1.00
- Q9KQU8 · AlphaFold monomer V2.0 prediction for fatty acid metabolism regulator protein (Q9KQU8) · a predicted model of the same protein · chain E against A, TM-score 0.96
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 Q9KQU8
- Elsewhere: RCSB PDB 4P9U · PDBe 4P9U · UniProt Q9KQU8
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