MolNFT v1 · #155314 · protein + DNA
Structural basis for DNA unwinding at forked dsdna by two coordinating PIF1 helicases
6L3G · DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP…: “Structural basis for DNA unwinding at forked dsdna by two coordinating PIF1 helicases”. X-ray diffraction, 3 ligands (ADP, ALF, MG), 14 pockets (best druggability…
- PDB
- 6L3G
- Type
- protein + DNA
- Length
- 847 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*TP*TP*TP*T)- 3')…
- UniProt
- A0A373G551
- Ligands
- ADP, ALF, MG
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*TP*TP*TP*T)- 3') | dna | 21 | — | — |
| A | ATP-dependent DNA helicase | protein | 413 | 35% helix, 23% strand | A0A373G551 |
| B | ATP-dependent DNA helicase | protein | 413 | 34% helix, 23% strand | A0A373G551 |
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
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.74 | 0.82 | 50 | empty |
| 2 | 729 | 0.72 | 0.79 | 57 | empty |
| 3 | 77 | 0.68 | 0.94 | 18 | empty |
| 4 | 228 | 0.56 | 0.78 | 35 | empty |
| 5 | 146 | 0.55 | 0.81 | 31 | ADP, MG, ALF |
Interfaces
3 interfaces between chains.
- D–A · 1084 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–B · 996 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 154 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6L3G · Structural Basis for DNA Unwinding at Forked dsDNA by two coordinating Pif1 helicases · the same entry in another collection · chain D against D, 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 A0A373G551
- Elsewhere: RCSB PDB 6L3G · PDBe 6L3G · UniProt A0A373G551
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