MolNFT v1 · #118946 · protein + DNA
Structure of bacteroides sp PIF1 complexed with tailed dsdna resulting in ssdna bound complex
5FHD · Uncharacterized protein: “Structure of bacteroides sp PIF1 complexed with tailed dsdna resulting in ssdna bound complex”. X-ray diffraction, 3 ligands (ADP, ALF, MG), 11 pockets (best druggability 0.74). MolNFT v1 #118946 on…
- 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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