MolNFT v1 · #163458 · protein + DNA
Crystal structure of helicase PIF1 from thermus oshimai in complex with ssdna (DT)18 and ADP-ALF4
6S3M · PIF1 helicase: “Crystal structure of helicase PIF1 from thermus oshimai in complex with ssdna (DT)18 and ADP-ALF4”. X-ray diffraction, 3 ligands (ADP, ALF, MG), 14 pockets (best druggability 0.86). MolNFT v1 #163458 on GenesisL1: 3D…
- PDB
- 6S3M
- Type
- protein + DNA
- Length
- 882 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*G)-3')
- UniProt
- K7RJ88
- Ligands
- ADP, ALF, MG
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | PIF1 helicase | protein | 436 | 35% helix, 23% strand | K7RJ88 |
| C, D | DNA (5'-D(P*TP*TP*TP*TP*TP*G)-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
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.86 | 0.87 | 108 | empty |
| 2 | 285 | 0.78 | 0.90 | 45 | empty |
| 3 | 70 | 0.72 | 0.96 | 21 | empty |
| 4 | 131 | 0.63 | 0.86 | 20 | empty |
| 5 | 93 | 0.51 | 0.83 | 21 | ADP, MG, ALF |
Interfaces
4 interfaces between chains.
- B–D · 857 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 836 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 791 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 32 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6S3M · Crystal structure of helicase Pif1 from Thermus oshimai in complex with ssDNA (dT)18 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 6S3M · PDBe 6S3M · UniProt K7RJ88
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