MolNFT v1 · #63401 · protein
Crystal structure of the effector domain of phnf from mycobacterium smegmatis
3F8L · Hth-type transcriptional repressor phnf: “Crystal structure of the effector domain of phnf from mycobacterium smegmatis”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.60). MolNFT v1 #63401 on GenesisL1: 3D…
- PDB
- 3F8L
- Type
- protein
- Length
- 653 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional repressor phnf
- UniProt
- A0QQ72
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Hth-type transcriptional repressor phnf | protein | 162 | 22% helix, 44% strand | A0QQ72 |
| B | Hth-type transcriptional repressor phnf | protein | 167 | 20% helix, 44% strand | A0QQ72 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.60 | 0.83 | 34 | empty |
| 2 | 121 | 0.38 | 0.74 | 23 | empty |
| 3 | 59 | 0.32 | 0.76 | 15 | GOL |
| 4 | 87 | 0.31 | 0.72 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1216 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1190 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 399 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3F8L · Crystal Structure of the Effector Domain of PhnF from Mycobacterium smegmatis · the same entry in another collection · chain A against A, TM-score 1.00
- A0QQ72 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor phnf (A0QQ72) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 A0QQ72
- Elsewhere: RCSB PDB 3F8L · PDBe 3F8L · UniProt A0QQ72
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