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Crystal structure of helicase PIF1 from thermus oshimai in complex with ssdna (DT)18 and ADP-VO4
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
- 6S3N
- 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*T)-3')
- UniProt
- K7RJ88
- Ligands
- ADP, MG, VO4
- Pockets
- 10 · 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*T)-3') | dna | 5 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- VO4 · Vanadate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.86 | 0.87 | 104 | empty |
| 2 | 266 | 0.77 | 0.90 | 41 | empty |
| 3 | 158 | 0.67 | 0.87 | 21 | empty |
| 4 | 112 | 0.53 | 0.83 | 20 | ADP, MG, VO4 |
| 5 | 90 | 0.51 | 0.84 | 18 | ADP, MG, VO4 |
Interfaces
4 interfaces between chains.
- A–C · 876 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–D · 870 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 785 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 65 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 6S3N · 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 6S3N · PDBe 6S3N · UniProt K7RJ88
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