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Structural basis for DNA unwinding at forked dsdna by two coordinating PIF1 helicases
Analyse Structural basis for DNA unwinding at forked dsdna by two coordinating PIF1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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