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Crystal structure of helicase PIF1 from thermus oshimai in complex with oligo ggtttggtttggtt
Analyse Crystal structure of helicase PIF1 from thermus oshimai in complex with oligo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BIL
- Type
- protein + DNA
- Length
- 886 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PIF1 helicase; DNA (5'-D(*GP*GP*TP*TP*TP*GP*GP*TP*TP*TP*GP*GP*TP*T)-3')
- UniProt
- K7RJ88
- Ligands
- ADP, ALF, MG, K
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | PIF1 helicase | protein | 436 | 35% helix, 24% strand | K7RJ88 |
| C | DNA (5'-D(*GP*GP*TP*TP*TP*GP*GP*TP*TP*TP*GP*GP*TP*T)-3') | dna | 14 | — | — |
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
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.84 | 0.87 | 87 | empty |
| 2 | 406 | 0.77 | 0.86 | 44 | empty |
| 3 | 98 | 0.76 | 0.97 | 20 | empty |
| 4 | 61 | 0.72 | 0.98 | 16 | empty |
| 5 | 58 | 0.70 | 0.97 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1262 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 1109 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 784 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7BIL · Crystal structure of helicase Pif1 from Thermus oshimai in complex with oligo… · 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 K7RJ88
- Elsewhere: RCSB PDB 7BIL · PDBe 7BIL · UniProt K7RJ88
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