Research workbench
Crystal structure of helicase PIF1 from thermus oshimai in complex with parallel G-quadruplex
Analyse Crystal structure of helicase PIF1 from thermus oshimai in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OAR
- Type
- protein + DNA
- Length
- 882 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PIF1 helicase; DNA (28-mer)
- Ligands
- ADP, ALF, K, MG
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PIF1 helicase | protein | 442 | 33% helix, 23% strand | — |
| B | PIF1 helicase | protein | 413 | 35% helix, 18% strand | — |
| C | DNA (28-mer) | dna | 27 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 3 copies · chains C
- 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.77 | 0.82 | 84 | empty |
| 2 | 729 | 0.77 | 0.81 | 68 | empty |
| 3 | 69 | 0.73 | 0.97 | 17 | empty |
| 4 | 112 | 0.64 | 0.88 | 19 | empty |
| 5 | 503 | 0.60 | 0.75 | 47 | K |
Interfaces
2 interfaces between chains.
- A–C · 1335 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–C · 924 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 7OAR · Crystal structure of helicase Pif1 from Thermus oshimai in complex with parallel… · 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
- Elsewhere: RCSB PDB 7OAR · PDBe 7OAR
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