MolNFT v1 · #174027 · protein + DNA
Crystal structure of helicase PIF1 from thermus oshimai in complex with oligo ggtttggtttggtt
7BIL · PIF1 helicase: “Crystal structure of helicase PIF1 from thermus oshimai in complex with oligo ggtttggtttggtt”. X-ray diffraction, 4 ligands (ADP, ALF, MG), 18 pockets (best druggability 0.84). MolNFT v1 #174027 on GenesisL1: 3D…
- 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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