MolNFT v1 · #163460 · protein + DNA
Crystal structure of helicase PIF1 from thermus oshimai in complex with ssdna (DT)18 and ADP
6S3O · PIF1 helicase: “Crystal structure of helicase PIF1 from thermus oshimai in complex with ssdna (DT)18 and ADP”. X-ray diffraction, 2 ligands (ADP, MG), 5 pockets (best druggability 0.81). MolNFT v1 #163460 on GenesisL1: 3D structure…
- PDB
- 6S3O
- Type
- protein + DNA
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PIF1 helicase; DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3')
- UniProt
- K7RJ88
- Ligands
- ADP, MG
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PIF1 helicase | protein | 436 | 36% helix, 23% strand | K7RJ88 |
| B | DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 7 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.81 | 0.83 | 112 | MG |
| 2 | 219 | 0.62 | 0.82 | 26 | empty |
| 3 | 88 | 0.36 | 0.75 | 20 | empty |
| 4 | 68 | 0.32 | 0.75 | 15 | empty |
| 5 | 55 | 0.30 | 0.75 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 876 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 6S3O · 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 6S3O · PDBe 6S3O · UniProt K7RJ88
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