MolNFT v1 · #151500 · protein
Crystal structure of human PIF1 helicase in complex with AMP-pnp, brominated crystal form.
6HPQ · ATP-dependent DNA helicase PIF1: “Crystal structure of human PIF1 helicase in complex with AMP-pnp, brominated crystal form.”. X-ray diffraction, 3 ligands (ANP, MG, BR), 9 pockets (best druggability 0.79). MolNFT v1 #151500 on…
- PDB
- 6HPQ
- Type
- protein
- Length
- 832 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
- ANP, MG, BR
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent DNA helicase PIF1 (EC 3.6.4.12) | protein | 416 | 36% helix, 22% strand | Q9H611 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- BR · Bromide ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.79 | 0.82 | 96 | empty |
| 2 | 671 | 0.77 | 0.82 | 84 | BR |
| 3 | 311 | 0.61 | 0.79 | 29 | ANP, MG |
| 4 | 243 | 0.60 | 0.80 | 30 | ANP, MG |
| 5 | 187 | 0.57 | 0.80 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 878 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6HPQ · Crystal structure of human Pif1 helicase in complex with AMP-PNP, brominated crystal form. · 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 0.98
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 6HPQ · PDBe 6HPQ · UniProt Q9H611
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