MolNFT v1 · #184541 · protein + DNA
Crystal structure of PIF1 helicase from candida albicans
7OTJ · ATP-dependent DNA helicase PIF1: “Crystal structure of PIF1 helicase from candida albicans”. X-ray diffraction, 5 ligands (ADP, ALF, K), 13 pockets (best druggability 0.83). MolNFT v1 #184541 on GenesisL1: 3D structure, binding…
- PDB
- 7OTJ
- Type
- protein + DNA
- Length
- 884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase PIF1; DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
- EC
- 3.6.4.12
- UniProt
- Q59RQ0
- Ligands
- ADP, ALF, K, MG, PO4
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA helicase PIF1 (EC 3.6.4.12) | protein | 438 | 36% helix, 22% strand | Q59RQ0 |
| B | ATP-dependent DNA helicase PIF1 (EC 3.6.4.12) | protein | 436 | 36% helix, 20% strand | Q59RQ0 |
| 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
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 10 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.83 | 0.84 | 102 | K |
| 2 | 531 | 0.76 | 0.84 | 64 | empty |
| 3 | 96 | 0.60 | 0.88 | 27 | ADP, ALF, MG |
| 4 | 213 | 0.58 | 0.80 | 25 | empty |
| 5 | 88 | 0.55 | 0.86 | 23 | ADP, ALF, MG |
Interfaces
4 interfaces between chains.
- A–B · 1149 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 785 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 771 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 65 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
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 Q59RQ0
- Elsewhere: RCSB PDB 7OTJ · PDBe 7OTJ · UniProt Q59RQ0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.