MolNFT v1 · #151504 · protein
Crystal structure of human PIF1 helicase in complex with ADP-ALF4
6HPU · ATP-dependent DNA helicase PIF1: “Crystal structure of human PIF1 helicase in complex with ADP-ALF4”. X-ray diffraction, 3 ligands (ADP, ALF, MG), 13 pockets (best druggability 0.71). MolNFT v1 #151504 on GenesisL1: 3D structure…
- PDB
- 6HPU
- Type
- protein
- Length
- 834 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase PIF1
- EC
- 3.6.4.12
- UniProt
- Q9H611
- Ligands
- ADP, ALF, MG
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA helicase PIF1 (EC 3.6.4.12) | protein | 418 | 32% helix, 20% strand | Q9H611 |
| B | ATP-dependent DNA helicase PIF1 (EC 3.6.4.12) | protein | 416 | 36% helix, 19% strand | Q9H611 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- 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
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 | 301 | 0.71 | 0.85 | 44 | empty |
| 2 | 450 | 0.71 | 0.81 | 54 | empty |
| 3 | 924 | 0.69 | 0.75 | 82 | empty |
| 4 | 368 | 0.62 | 0.78 | 39 | ADP, ALF, MG |
| 5 | 246 | 0.61 | 0.81 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 993 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6HPU · Crystal structure of human Pif1 helicase in complex with ADP-AlF4 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H611 · AlphaFold monomer V2.0 prediction for ATP-dependent DNA helicase PIF1 (Q9H611) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9H611
- Elsewhere: RCSB PDB 6HPU · PDBe 6HPU · UniProt Q9H611
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