Research workbench
Crystal structure of phnf from mycobacterium smegmatis
Analyse Crystal structure of phnf from mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F8M
- Type
- protein
- Length
- 455 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gntr-family protein transcriptional regulator
- UniProt
- A0QQ72
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gntr-family protein transcriptional regulator | protein | 230 | 31% helix, 36% strand | A0QQ72 |
| B | Gntr-family protein transcriptional regulator | protein | 225 | 30% helix, 37% strand | A0QQ72 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · 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 | 64 | 0.66 | 0.94 | 23 | empty |
| 2 | 88 | 0.63 | 0.90 | 29 | empty |
| 3 | 363 | 0.55 | 0.74 | 36 | GOL |
| 4 | 287 | 0.51 | 0.74 | 37 | GOL |
| 5 | 94 | 0.45 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1608 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3F8M · Crystal Structure 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 B against A, TM-score 0.74
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 3F8M · PDBe 3F8M · UniProt A0QQ72
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