Research workbench
Crystal structure of helicase PIF1 from thermus oshimai in complex with ssdna (DT)18 and ADP
Analyse Crystal structure of helicase PIF1 from thermus oshimai in complex with ssdna… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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