Research workbench
Structure of bacteroides sp PIF1 complexed with tailed dsdna resulting in ssdna bound complex
Analyse Structure of bacteroides sp PIF1 complexed with tailed dsdna resulting in ssdna… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FHD
- Type
- protein + DNA
- Length
- 829 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; DNA (5'- D(*TP*TP*TP*TP*TP*TP*TP*CP*CP*GP*GP*GP*GP*CP*CP*GP*CP*GP…
- UniProt
- D1JM21
- Ligands
- ADP, ALF, MG
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 414 | 35% helix, 23% strand | D1JM21 |
| C | DNA (5'- D(*TP*TP*TP*TP*TP*TP*TP*CP*CP*GP*GP*GP*GP*CP*CP*GP*CP*GP*C)-3') | dna | 8 | — | — |
| E | DNA (5'- D(*TP*TP*TP*TP*TP*TP*TP*CP*CP*GP*GP*GP*GP*CP*CP*GP*CP*GP*C)-3') | dna | 7 | — | — |
| B | Uncharacterized protein | protein | 400 | 35% helix, 19% strand | D1JM21 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.74 | 0.79 | 70 | empty |
| 2 | 531 | 0.71 | 0.80 | 56 | empty |
| 3 | 424 | 0.63 | 0.77 | 37 | empty |
| 4 | 363 | 0.61 | 0.78 | 47 | ADP, MG, ALF |
| 5 | 161 | 0.54 | 0.80 | 28 | ADP, MG, ALF |
Interfaces
3 interfaces between chains.
- A–C · 1154 Ų buried · 16 hydrogen bonds · protein-nucleic
- E–B · 1070 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 405 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5FHD · Structure of Bacteroides sp Pif1 complexed with tailed dsDNA resulting in ssDNA bound… · 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 5FHD · PDBe 5FHD · UniProt D1JM21
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