MolNFT v1 · #163453 · protein + DNA
Crystal structure of helicase PIF1 from thermus oshimai in complex with ADP-ALF4 and (DT)7DS11BP
6S3H · PIF1 helicase: “Crystal structure of helicase PIF1 from thermus oshimai in complex with ADP-ALF4 and (DT)7DS11BP”. X-ray diffraction, 3 ligands (ADP, ALF, MG), 16 pockets (best druggability 0.77). MolNFT v1 #163453 on GenesisL1: 3D…
- PDB
- 6S3H
- Type
- protein + DNA
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PIF1 helicase; DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
- UniProt
- K7RJ88
- Ligands
- ADP, ALF, MG
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PIF1 helicase | protein | 422 | 35% helix, 21% strand | K7RJ88 |
| B | PIF1 helicase | protein | 423 | 33% helix, 22% strand | K7RJ88 |
| D | DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3') | dna | 6 | — | — |
| E | DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3') | dna | 5 | — | — |
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
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.77 | 0.96 | 19 | empty |
| 2 | 61 | 0.69 | 0.96 | 20 | empty |
| 3 | 505 | 0.69 | 0.79 | 54 | empty |
| 4 | 148 | 0.65 | 0.87 | 25 | empty |
| 5 | 99 | 0.53 | 0.84 | 20 | MG, ADP, ALF |
Interfaces
3 interfaces between chains.
- A–D · 1016 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–E · 804 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 429 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6S3H · Crystal structure of helicase Pif1 from Thermus oshimai in complex with ADP-AlF4 and… · 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 6S3H · PDBe 6S3H · UniProt K7RJ88
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