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Crystal structure of helicase PIF1 from thermus oshimai in complex with ssdna (DT)18 and ADP-MGF4
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
- 6S3I
- Type
- protein + DNA
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PIF1 helicase; DNA (5'-D(P*TP*TP*TP*TP*T)-3')
- UniProt
- K7RJ88
- Ligands
- ADP, MF4, MG
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PIF1 helicase | protein | 434 | 32% helix, 21% strand | K7RJ88 |
| C | DNA (5'-D(P*TP*TP*TP*TP*T)-3') | dna | 5 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MF4 · Tetrafluoromagnesate(2-) · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.72 | 0.89 | 37 | empty |
| 2 | 79 | 0.59 | 0.88 | 20 | empty |
| 3 | 229 | 0.56 | 0.78 | 31 | empty |
| 4 | 89 | 0.50 | 0.83 | 19 | ADP, MG, MF4 |
| 5 | 125 | 0.44 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–C · 919 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 6S3I · 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 6S3I · PDBe 6S3I · UniProt K7RJ88
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