Research workbench
Crystal structure of bacteroides PIF1 bound to ssdna
Analyse Crystal structure of bacteroides PIF1 bound to ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FHE
- Type
- protein + DNA
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
- UniProt
- D1JM21
- Ligands
- ADP, ALF, MG
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 426 | 28% helix, 25% strand | D1JM21 |
| C | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 6 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ALF · Tetrafluoroaluminate ion · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.71 | 0.79 | 55 | empty |
| 2 | 121 | 0.47 | 0.79 | 23 | ADP, ALF |
| 3 | 162 | 0.47 | 0.76 | 24 | empty |
| 4 | 127 | 0.43 | 0.76 | 21 | empty |
| 5 | 116 | 0.43 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–C · 963 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 5FHE · Crystal structure of Bacteroides Pif1 bound to ssDNA · the same entry in another collection · chain A against A, TM-score 1.00
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 D1JM21
- Elsewhere: RCSB PDB 5FHE · PDBe 5FHE · UniProt D1JM21
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